tooltip.select_highlighted_columns = Press B to mark highlighted columns, Ctrl-(or Cmd)-B to toggle, and Alt-B to mark all but highlighted columns
action.deselect_all = Deselect all
action.invert_selection = Invert selection
+action.filter_by_evalue = Filter by E-Value
+action.filter_by_score = Filter by Score
action.using_jmol = Using Jmol
action.link = Link
action.group_link = Group Link
exception.ranml_invalid_file = Invalid RNAML file ({0})
exception.ranml_problem_parsing_data = Problem parsing data as RNAML ({0})
exception.pfam_no_sequences_found = No sequences found (PFAM input)
+exception.hmmer_no_valid_sequences_found = No valid sequences found
exception.stockholm_invalid_format = This file is not in valid STOCKHOLM format: First line does not contain '# STOCKHOLM'
exception.couldnt_parse_sequence_line = Could not parse sequence line: {0}
exception.unknown_annotation_detected = Unknown annotation detected: {0} {1}
*/
private long invalidrnastruc = -2;
+ private double bitScore;
+
+ private double eValue;
+
/**
* Updates the _rnasecstr field Determines the positions that base pair and
* the positions of helices based on secondary structure from a Stockholm file
return aa;
}
+ public double getBitScore()
+ {
+ return bitScore;
+ }
+
+ public void setBitScore(double bitScore)
+ {
+ this.bitScore = bitScore;
+ }
+
+ public double getEValue()
+ {
+ return eValue;
+ }
+
+ public void setEValue(double eValue)
+ {
+ this.eValue = eValue;
+ }
+
}
}
return true;
}
+
+ @Override
+ protected void filterByEValue_actionPerformed()
+ {
+ viewport.filterByEvalue(inputDouble("Enter E-Value Cutoff"));
+ }
+
+ @Override
+ protected void filterByScore_actionPerformed()
+ {
+ viewport.filterByScore(inputDouble("Enter Bit Score Threshold"));
+ }
+
+ private double inputDouble(String message)
+ {
+ String str = null;
+ Double d = null;
+ while(d == null || d <= 0)
+ {
+ str = JOptionPane.showInputDialog(this.alignPanel, message);
+ try
+ {
+ d = Double.valueOf(str);
+ }
+ catch (NumberFormatException e)
+ {
+ }
+ }
+ return d;
+ }
/**
* Checks if the alignment contains the required number of sequences.
}
/**
- * A helper method that deletes any HMM consensus sequence from the given
- * collection, and from the parent alignment if <code>ac</code> is a subgroup
- *
- * @param ac
- */
- void deleteHmmSequences(AnnotatedCollectionI ac)
- {
- List<SequenceI> hmmSeqs = ac.getHmmSequences();
- for (SequenceI hmmSeq : hmmSeqs)
- {
- if (ac instanceof SequenceGroup)
- {
- ((SequenceGroup) ac).deleteSequence(hmmSeq, false);
- AnnotatedCollectionI context = ac.getContext();
- if (context != null && context instanceof AlignmentI)
- {
- ((AlignmentI) context).deleteSequence(hmmSeq);
- }
- }
- else
- {
- ((AlignmentI) ac).deleteSequence(hmmSeq);
- }
- }
- }
-
- /**
* Constructs and executes the hmmbuild command as a separate process
*
* @param sequencesFile
&& !"".equals(line))
{
SequenceI seq = seqs[index];
- AlignmentAnnotation pp = seq
- .getAlignmentAnnotations("", "Posterior Probability")
- .get(0);
Scanner scanner = new Scanner(line);
- String str = scanner.next();
- addScoreAnnotation(str, seq, "hmmsearch E-value",
- "Full sequence E-value", pp);
- str = scanner.next();
- addScoreAnnotation(str, seq, "hmmsearch Score",
- "Full sequence bit score", pp);
- seq.removeAlignmentAnnotation(pp);
+ String evalue = scanner.next();
+ String score = scanner.next();
+ addScoreAnnotations(evalue, score, seq);
scanner.close();
line = br.readLine();
index++;
br.close();
}
- /**
- * A helper method that adds one score-only (non-positional) annotation to a
- * sequence
- *
- * @param value
- * @param seq
- * @param label
- * @param description
- */
- protected void addScoreAnnotation(String value, SequenceI seq,
- String label, String description)
- {
- addScoreAnnotation(value, seq, label, description, null);
- }
- /**
- * A helper method that adds one score-only (non-positional) annotation to a
- * sequence
- *
- * @param value
- * @param seq
- * @param label
- * @param description
- * @param pp
- * existing posterior probability annotation - values copied to new
- * annotation row
- */
- protected void addScoreAnnotation(String value, SequenceI seq,
- String label, String description, AlignmentAnnotation pp)
+ 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 = null;
- if (pp == null)
- {
- new AlignmentAnnotation(label,
+ AlignmentAnnotation annot = new AlignmentAnnotation(label,
description, null);
- }
- else
- {
- annot = new AlignmentAnnotation(pp);
- annot.label = label;
- annot.description = description;
- }
+
+ annot.label = label;
+ annot.description = description;
+
annot.setCalcId(HMMSEARCH);
- double eValue = Double.parseDouble(value);
- annot.setScore(eValue);
+
+ 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 " + value);
+ System.err.println("Error parsing " + label + " from " + eValue
+ + " & " + bitScore);
}
}
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.Annotation;
import jalview.datamodel.HiddenMarkovModel;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.JvOptionPane;
/**
* Exports an alignment, and reference (RF) annotation if present, to the
- * specified file, in Stockholm format
+ * specified file, in Stockholm format, removing all HMM sequences
*
* @param seqs
* @param toFile
writer.close();
}
- public void exportFasta(SequenceI[] seqs, File toFile)
+ /**
+ * Exports the given alignment withotu any anotations to a fasta file
+ *
+ * @param seqs
+ * @param toFile
+ */
+ public void exportFasta(AlignmentI al, File toFile)
{
FastaFile file = new FastaFile();
- String output = file.print(seqs, false);
+
+ String output = file.print(al.getSequencesArray(), false);
PrintWriter writer;
try
{
return path;
}
+
+ /**
+ * A helper method that deletes any HMM consensus sequence from the given
+ * collection, and from the parent alignment if <code>ac</code> is a subgroup
+ *
+ * @param ac
+ */
+ void deleteHmmSequences(AnnotatedCollectionI ac)
+ {
+ List<SequenceI> hmmSeqs = ac.getHmmSequences();
+ for (SequenceI hmmSeq : hmmSeqs)
+ {
+ if (ac instanceof SequenceGroup)
+ {
+ ((SequenceGroup) ac).deleteSequence(hmmSeq, false);
+ AnnotatedCollectionI context = ac.getContext();
+ if (context != null && context instanceof AlignmentI)
+ {
+ ((AlignmentI) context).deleteSequence(hmmSeq);
+ }
+ }
+ else
+ {
+ ((AlignmentI) ac).deleteSequence(hmmSeq);
+ }
+ }
+ }
}
*/
databaseFile = FileUtils.createTempFile("database", ".fa");
AlignmentI al = af.getViewport().getAlignment();
- exportFasta(al.getSequencesArray(), databaseFile);
+ deleteHmmSequences(al);
+ exportFasta(al, databaseFile);
}
args.add(getFilePath(seqFile, true));
&& !"".equals(line))
{
SequenceI seq = seqs[index];
- AlignmentAnnotation pp = null;
- if (seq.getAlignmentAnnotations("", "Posterior Probability")
- .size() != 0)
- {
- pp = seq.getAlignmentAnnotations("", "Posterior Probability")
- .get(0);
- }
+
Scanner scanner = new Scanner(line);
- String str = scanner.next();
- str = scanner.next();
- addScoreAnnotation(str, seq, "jackhmmer E-value",
- "Full sequence E-value", pp);
- str = scanner.next();
- addScoreAnnotation(str, seq, "jackhmmer Score",
- "Full sequence bit score", pp);
- seq.removeAlignmentAnnotation(pp);
+ String evalue = scanner.next();
+ evalue = scanner.next();
+ String score = scanner.next();
+ addScoreAnnotations(evalue, score, seq);
scanner.close();
line = br.readLine();
index++;
br.close();
}
- /**
- * A helper method that adds one score-only (non-positional) annotation to a
- * sequence
- *
- * @param value
- * @param seq
- * @param label
- * @param description
- */
- protected void addScoreAnnotation(String value, SequenceI seq,
- String label, String description)
+ protected void addScoreAnnotations(String eValue, String bitScore,
+ SequenceI seq)
{
- addScoreAnnotation(value, seq, label, description, null);
- }
+ String label = "Search Scores";
+ String description = "Full sequence bit score and E-Value";
- /**
- * A helper method that adds one score-only (non-positional) annotation to a
- * sequence
- *
- * @param value
- * @param seq
- * @param label
- * @param description
- * @param pp
- * existing posterior probability annotation - values
- * copied to new annotation row
- */
- protected void addScoreAnnotation(String value, SequenceI seq,
- String label, String description, AlignmentAnnotation pp)
- {
try
{
- AlignmentAnnotation annot = null;
- if (pp == null)
- {
- annot = new AlignmentAnnotation(label, description, null);
- }
- else
- {
- annot = new AlignmentAnnotation(pp);
- annot.label = label;
- annot.description = description;
- }
+ AlignmentAnnotation annot = new AlignmentAnnotation(label,
+ description, null);
+
+ annot.label = label;
+ annot.description = description;
+
annot.setCalcId(JACKHMMER);
- double eValue = Double.parseDouble(value);
- annot.setScore(eValue);
+
+ double dEValue = Double.parseDouble(eValue);
+ annot.setEValue(dEValue);
+
+ double dBitScore = Double.parseDouble(bitScore);
+ annot.setEValue(dBitScore);
+
annot.setSequenceRef(seq);
seq.addAlignmentAnnotation(annot);
} catch (NumberFormatException e)
{
- System.err.println("Error parsing " + label + " from " + value);
+ System.err.println("Error parsing " + label + " from " + eValue
+ + " & " + bitScore);
}
}
+
+
}
* Comparator to order DBRefEntry by Source + accession id (case-insensitive),
* with 'Primary' sources placed before others, and 'chromosome' first of all
*/
- private static Comparator<DBRefEntry> comparator = new Comparator<DBRefEntry>()
+ private static Comparator<DBRefEntry> comparator = new Comparator<>()
{
@Override
maxWidth = Math.max(maxWidth, sz);
}
}
+
+ sb.append("<br>");
+ if (sequence.getAnnotation("Search Scores") != null)
+ {
+ String eValue = " E-Value: "
+ + sequence.getAnnotation("Search Scores")[0].getEValue();
+ String bitScore = " Bit Score: "
+ + sequence.getAnnotation("Search Scores")[0].getBitScore();
+ sb.append(eValue);
+ sb.append("<br>");
+ sb.append(bitScore);
+ maxWidth = Math.max(maxWidth, eValue.length());
+ maxWidth = Math.max(maxWidth, bitScore.length());
+ }
+ sb.append("<br>");
sb.append("</i>");
+
return maxWidth;
}
}
};
addMenuActionAndAccelerator(keyStroke, removeRedundancyMenuItem, al);
+
+ JMenuItem filterByEValue = new JMenuItem(
+ MessageManager.getString("action.filter_by_evalue"));
+ filterByEValue.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterByEValue_actionPerformed();
+ }
+
+ });
+
+ JMenuItem filterByScore = new JMenuItem(
+ MessageManager.getString("action.filter_by_score"));
+ filterByScore.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ filterByScore_actionPerformed();
+ }
+
+ });
JMenuItem pairwiseAlignmentMenuItem = new JMenuItem(
MessageManager.getString("action.pairwise_alignment"));
selectHighlightedColumns_actionPerformed(actionEvent);
}
};
+ JMenuItem Filter = new JMenuItem(
+ MessageManager.getString("action.select_highlighted_columns"));
+ selectHighlighted.setToolTipText(
+ MessageManager.getString("tooltip.select_highlighted_columns"));
+ al = new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent actionEvent)
+ {
+ selectHighlightedColumns_actionPerformed(actionEvent);
+ }
+ };
selectHighlighted.addActionListener(al);
JMenu tooltipSettingsMenu = new JMenu(
MessageManager.getString("label.sequence_id_tooltip"));
// editMenu.add(justifyRightMenuItem);
// editMenu.addSeparator();
editMenu.add(padGapsMenuitem);
+ editMenu.addSeparator();
+ editMenu.add(filterByEValue);
+ editMenu.add(filterByScore);
showMenu.add(showAllColumns);
showMenu.add(showAllSeqs);
{
}
+ protected void filterByEValue_actionPerformed()
+ {
+ }
+
+ protected void filterByScore_actionPerformed()
+ {
+ }
+
protected void scaleRight_actionPerformed(ActionEvent e)
{
}
codingComplement.setUpdateStructures(needToUpdateStructureViews);
}
}
+
+ /**
+ * Filters out sequences with an eValue higher than the specified value. The
+ * filtered sequences are hidden or deleted. Sequences with no eValues are also
+ * filtered out.
+ *
+ * @param eValue
+ * @param delete
+ */
+ public void filterByEvalue(double eValue)
+ {
+ for (SequenceI seq : alignment.getSequencesArray())
+ {
+ if ((seq.getAnnotation("Search Scores") == null
+ || seq.getAnnotation("Search Scores")[0].getEValue() > eValue)
+ && seq.getHMM() == null)
+ {
+ hideSequence(new SequenceI[] { seq });
+ }
+ }
+ }
+
+ /**
+ * Filters out sequences with an score lower than the specified value. The
+ * filtered sequences are hidden or deleted.
+ *
+ * @param score
+ * @param delete
+ */
+ public void filterByScore(double score)
+ {
+ for (SequenceI seq : alignment.getSequencesArray())
+ {
+ if ((seq.getAnnotation("Search Scores") == null
+ || seq.getAnnotation("Search Scores")[0]
+ .getBitScore() < score)
+ && seq.getHMM() == null)
+ {
+ hideSequence(new SequenceI[] { seq });
+ }
+ }
+ }
}
git://source.jalview.org / jalview.git / commitdiff