label.trim_termini_desc = If true, non-matching regions on either end of the resulting alignment are removed.
label.no_of_sequences = Number of sequences returned
label.reporting_cutoff = Reporting Cut-off
+label.inclusion_threshold = Inlcusion Threshold
label.freq_alignment = Use alignment background frequencies
label.freq_uniprot = Use Uniprot background frequencies
label.hmmalign_options = hmmalign options
label.new_returned = new sequences returned
label.use_accessions = Return Accessions
label.check_for_new_sequences = Return Number of New Sequences
-label.seq_evalue = Sequence E-value Cut-off
label.evalue = E-Value
-label.seq_score = Sequence Score Threshold
-label.dom_evalue = Domain E-value Cut-off
-label.dom_score = Domain Score Threshold
+label.reporting_seq_evalue = Reporting Sequence E-value Cut-off
+label.reporting_seq_score = Reporting Sequence Score Threshold
+label.reporting_dom_evalue = Reporting Domain E-value Cut-off
+label.reporting_dom_score = Reporting Domain Score Threshold
+label.inclusion_seq_evalue = Inclusion Sequence E-value Cut-off
+label.inclusion_seq_score = Inclusion Sequence Score Threshold
+label.inclusion_dom_evalue = Inclusion Domain E-value Cut-off
+label.inclusion_dom_score = Inclusion Domain Score Threshold
label.number_of_results_desc = The maximum number of hmmsearch results to display
label.auto_align_seqs_desc = If true, all fetched sequences will be aligned to the hidden Markov model with which the search was performed
label.check_for_new_sequences_desc = Display number of new sequences returned from hmmsearch compared to the previous alignment
label.use_accessions_desc = If true, the accession number of each sequence is returned, rather than that sequence's name
-label.seq_e_value_desc = The E-value cutoff for returned sequences (hmmsearch -E)
-label.seq_score_desc = The score threshold for returned sequences (hmmsearch -T)
-label.dom_e_value_desc = The E-value cutoff for returned domains (hmmsearch --domE)
-label.dom_score_desc = The score threshold for returned domains (hmmsearch --domT)
+label.reporting_seq_e_value_desc = The E-value cutoff for returned sequences
+label.reporting_seq_score_desc = The score threshold for returned sequences
+label.reporting_dom_e_value_desc = The E-value cutoff for returned domains
+label.reporting_dom_score_desc = The score threshold for returned domains
+label.inclusion_seq_e_value_desc = Sequences with an E-value less than this cut-off are classed as significant
+label.inclusion_seq_score_desc = Sequences with a bit score greater than this threshold are classed as significant
+label.inclusion_dom_e_value_desc = Domains with an E-value less than this cut-off are classed as significant
+label.inclusion_dom_score_desc = Domains with a bit score greater than this threshold are classed as significant
label.add_database = Add Database
label.this_alignment = This alignment
warn.invalid_format = This is not a valid database file format. The current supported formats are Fasta, Stockholm and Pfam.
100, 0, 100000));
args.add(new RadioChoiceParameter(
MessageManager.getString(HMMSearch.REPORTING_CUTOFF_KEY), null,
- Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_NONE),
- MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
+ Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
MessageManager.getString(HMMSearch.CUTOFF_EVALUE)));
args.add(new LogarithmicParameter(
- MessageManager.getString(HMMSearch.SEQ_EVALUE_KEY),
- MessageManager.getString("label.seq_e_value_desc"), false, 1D,
+ MessageManager.getString(HMMSearch.REPORTING_SEQ_EVALUE_KEY),
+ MessageManager.getString("label.reporting_seq_e_value_desc"),
+ false, 1D,
1E-100, 10D));
args.add(new LogarithmicParameter(
- MessageManager.getString(HMMSearch.DOM_EVALUE_KEY),
- MessageManager.getString("label.dom_e_value_desc"), false, 1D,
+ MessageManager.getString(HMMSearch.REPORTING_DOM_EVALUE_KEY),
+ MessageManager.getString("label.reporting_dom_e_value_desc"),
+ false, 1D,
1E-100, 10D));
args.add(
new DoubleParameter(
- MessageManager.getString(HMMSearch.SEQ_SCORE_KEY),
- MessageManager.getString("label.seq_score_desc"), false,
+ MessageManager
+ .getString(HMMSearch.REPORTING_SEQ_SCORE_KEY),
+ MessageManager.getString(
+ "label.reporting_seq_score_desc"),
+ false,
0d, 0d, 1000d));
args.add(
new DoubleParameter(
- MessageManager.getString(HMMSearch.DOM_SCORE_KEY),
- MessageManager.getString("label.dom_score_desc"), false,
+ MessageManager
+ .getString(HMMSearch.REPORTING_DOM_SCORE_KEY),
+ MessageManager.getString(
+ "label.reporting_dom_score_desc"),
+ false,
0d, 0d, 1000d));
+ args.add(new RadioChoiceParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_THRESHOLD_KEY),
+ null,
+ Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
+ MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
+ MessageManager.getString(HMMSearch.CUTOFF_EVALUE)));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_SEQ_EVALUE_KEY),
+ MessageManager.getString("label.inclusion_seq_e_value_desc"),
+ false, 1D,
+ 1E-100, 10D));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_DOM_EVALUE_KEY),
+ MessageManager.getString("label.inclusion_dom_e_value_desc"),
+ false, 1D,
+ 1E-100, 10D));
+ args.add(new DoubleParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_SEQ_SCORE_KEY),
+ MessageManager.getString("label.inclusion_seq_score_desc"),
+ false, 0d, 0d,
+ 1000d));
+ args.add(new DoubleParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_DOM_SCORE_KEY),
+ MessageManager.getString("label.inclusion_dom_score_desc"),
+ false, 0d, 0d,
+ 1000d));
}
/**
MessageManager.getString(JackHMMER.CUTOFF_SCORE)),
MessageManager.getString(JackHMMER.CUTOFF_EVALUE)));
args.add(new LogarithmicParameter(
- MessageManager.getString(JackHMMER.SEQ_EVALUE_KEY),
- MessageManager.getString("label.seq_e_value_desc"), false, 1D,
+ MessageManager.getString(JackHMMER.REPORTING_SEQ_EVALUE_KEY),
+ MessageManager.getString("label.reporting_seq_e_value_desc"),
+ false, 1D,
1E-38, 10D));
args.add(new LogarithmicParameter(
- MessageManager.getString(JackHMMER.DOM_EVALUE_KEY),
- MessageManager.getString("label.dom_e_value_desc"), false, 1D,
+ MessageManager.getString(JackHMMER.REPORTING_DOM_EVALUE_KEY),
+ MessageManager.getString(
+ "label.reporting_seq_dom_e_value_desc"),
+ false, 1D,
1E-38, 10D));
args.add(new DoubleParameter(
- MessageManager.getString(JackHMMER.SEQ_SCORE_KEY),
- MessageManager.getString("label.seq_score_desc"), false, 0d, 0d,
+ MessageManager.getString(JackHMMER.REPORTING_SEQ_SCORE_KEY),
+ MessageManager.getString("label.reporting_seq_seq_score_desc"),
+ false, 0d, 0d,
1000d));
args.add(new DoubleParameter(
- MessageManager.getString(JackHMMER.DOM_SCORE_KEY),
- MessageManager.getString("label.dom_score_desc"), false, 0d, 0d,
+ MessageManager.getString(JackHMMER.REPORTING_DOM_SCORE_KEY),
+ MessageManager.getString("label.reporting_seq_dom_score_desc"),
+ false, 0d, 0d,
1000d));
+ args.add(new RadioChoiceParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_THRESHOLD_KEY),
+ null,
+ Arrays.asList(MessageManager.getString(HMMSearch.CUTOFF_EVALUE),
+ MessageManager.getString(HMMSearch.CUTOFF_SCORE)),
+ MessageManager.getString(HmmerCommand.CUTOFF_EVALUE)));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_SEQ_EVALUE_KEY),
+ MessageManager.getString("label.inclusion_seq_e_value_desc"),
+ false, 1D, 1E-100, 10D));
+ args.add(new LogarithmicParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_DOM_EVALUE_KEY),
+ MessageManager.getString("label.inclusion_dom_e_value_desc"),
+ false, 1D, 1E-100, 10D));
+ args.add(new DoubleParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_SEQ_SCORE_KEY),
+ MessageManager.getString("label.inclusion_seq_score_desc"),
+ false, 0d, 0d, 1000d));
+ args.add(new DoubleParameter(
+ MessageManager.getString(HMMSearch.INCLUSION_DOM_SCORE_KEY),
+ MessageManager.getString("label.inclusion_dom_score_desc"),
+ false, 0d, 0d, 1000d));
}
/**
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
-import java.util.Hashtable;
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;
int seqsToReturn = Integer.MAX_VALUE;
- boolean searchAlignment = true;
-
- SequenceI[] seqs;
-
- private String databaseName;
-
- Hashtable sequencesHash;
/**
* Constructor for the HMMSearchThread
return runCommand(args);
}
- /**
- * 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 hmmFile
- * @throws IOException
- */
- protected void buildArguments(List<String> args, File searchOutputFile,
- File hitsAlignmentFile, File hmmFile) throws IOException
- {
- args.add("-o");
- args.add(getFilePath(searchOutputFile, true));
- args.add("-A");
- args.add(getFilePath(hitsAlignmentFile, true));
-
- 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;
- databaseName = "Alignment";
-
- if (params != null)
- {
- for (ArgumentI arg : params)
- {
- String name = arg.getName();
- if (MessageManager.getString(NUMBER_OF_RESULTS_KEY)
- .equals(name))
- {
- seqsToReturn = Integer.parseInt(arg.getValue());
- }
- else if (MessageManager.getString(AUTO_ALIGN_SEQS_KEY)
- .equals(name))
- {
- realign = true;
- }
- else if (MessageManager.getString(USE_ACCESSIONS_KEY)
- .equals(name))
- {
- args.add("--acc");
- }
- else 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(TRIM_TERMINI_KEY)
- .equals(name))
- {
- trim = true;
- }
- else if (MessageManager.getString(DATABASE_KEY).equals(name))
- {
- databaseFile = new File(arg.getValue());
- if (!arg.getValue().isEmpty())
- {
- searchAlignment = false;
- }
- }
- else if (MessageManager.getString(RETURN_N_NEW_SEQ).equals(name))
- {
- returnNoOfNewSeqs = true;
- }
- }
- }
-
- 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,
- * excluding any HMM consensus sequences it contains
- */
- 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(hmmFile, true));
- args.add(getFilePath(databaseFile, true));
- }
/**
* Imports the data from the temporary file to which the output of hmmsearch
}
}
- /**
- * Reads in the scores table output by hmmsearch 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();
- String score = scanner.next();
- checkSequenceOrder(index, scanner);
- SequenceI seq = seqs[index];
- addScoreAnnotations(evalue, score, seq);
- scanner.close();
- line = br.readLine();
- index++;
- }
-
- br.close();
- }
-
-
- 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(HMMSEARCH);
-
- 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);
- }
- }
-
- private void checkSequenceOrder(int index, Scanner scanner)
- {
- String seqName = null;
-
- for (int i = 0; i < 8; i++)
- {
- seqName = scanner.next();
- }
-
- if (!seqs[index].getName().equals(seqName))
- {
- SequenceI temp = seqs[index];
-
- for (int j = 0; j < seqs.length; j++)
- {
- if (seqs[j].getName().equals(seqName))
- {
- seqs[index] = seqs[j];
- seqs[j] = temp;
- break;
- }
- }
- }
- }
-
}
static final String CUTOFF_EVALUE = "label.evalue";
- static final String SEQ_EVALUE_KEY = "label.seq_evalue";
+ static final String REPORTING_SEQ_EVALUE_KEY = "label.reporting_seq_evalue";
- static final String DOM_EVALUE_KEY = "label.dom_evalue";
+ static final String REPORTING_DOM_EVALUE_KEY = "label.reporting_dom_evalue";
- static final String SEQ_SCORE_KEY = "label.seq_score";
+ static final String REPORTING_SEQ_SCORE_KEY = "label.reporting_seq_score";
- static final String DOM_SCORE_KEY = "label.dom_score";
+ static final String REPORTING_DOM_SCORE_KEY = "label.reporting_dom_score";
+
+ static final String INCLUSION_SEQ_EVALUE_KEY = "label.inclusion_seq_evalue";
+
+ static final String INCLUSION_DOM_EVALUE_KEY = "label.inclusion_dom_evalue";
+
+ static final String INCLUSION_SEQ_SCORE_KEY = "label.inclusion_seq_score";
+
+ static final String INCLUSION_DOM_SCORE_KEY = "label.inclusion_dom_score";
static final String ARG_TRIM = "--trim";
+ static final String INCLUSION_THRESHOLD_KEY = "label.inclusion_threshold";
+
/**
* Constructor
*
import jalview.bin.Cache;
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;
/**
* Constructor for the JackhmmerThread
}
/**
- * 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.
*/
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);
- }
- }
--- /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()
+ {
+ }
+
+ /**
+ * 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();
+
+ if (evalue.equals("+") || evalue.equals("-"))
+ {
+ evalue = scanner.next();
+ }
+
+ String score = scanner.next();
+ checkSequenceOrder(index, scanner);
+ SequenceI seq = seqs[index];
+ addScoreAnnotations(evalue, score, seq);
+ scanner.close();
+ line = br.readLine();
+ index++;
+ }
+
+ br.close();
+ }
+
+ void checkSequenceOrder(int index, Scanner scanner)
+ {
+ String seqName = null;
+
+ for (int i = 0; i < 7; i++)
+ {
+ seqName = scanner.next();
+ }
+
+ if (!seqs[index].getName().equals(seqName))
+ {
+ SequenceI temp = seqs[index];
+
+ for (int j = 0; j < seqs.length; j++)
+ {
+ if (seqs[j].getName().equals(seqName))
+ {
+ seqs[index] = seqs[j];
+ seqs[j] = temp;
+ break;
+ }
+ }
+ }
+ }
+
+ 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("-o");
+ 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;
+ }
+ }
+ }
+ }
+
+ 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));
+ }
+}
.log(getHmm().getMatchEmissionProbability(column, symbol)
/ hmm.getBackgroundFrequencies().get(symbol));
- if (!probabilities.get(symbol).get(lengthBin)
+ if (!probabilities.containsKey(symbol)
+ || !probabilities.get(symbol).get(lengthBin)
.containsKey(format(llr)))
{
- return Color.white;
+ return new Color(140, 140, 140);
}
git://source.jalview.org / jalview.git / commitdiff