if (format.equalsIgnoreCase("Jalview"))
{
features = formatter.printJalviewFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols());
+ .getSequencesArray(), getDisplayedFeatureCols(), true);
}
else
{
features = formatter.printGffFormat(viewport.getAlignment()
- .getSequencesArray(), getDisplayedFeatureCols());
+ .getSequencesArray(), getDisplayedFeatureCols(), true);
}
if (displayTextbox)
/*
* else make a copy of the list, and remove any null value just in case,
* as it would cause errors looking up the features Map
+ * sort in alphabetical order for consistent output behaviour
*/
List<String> types = new ArrayList<String>(Arrays.asList(type));
types.remove(null);
+ Collections.sort(types);
return types;
}
boolean includeNonPositional = ap.av.isShowNPFeats();
if (GFFFormat.isSelected())
{
- text = formatter.printGffFormat(sequences, featureColours, true,
+ text = formatter.printGffFormat(sequences, featureColours,
includeNonPositional);
}
else
{
text = formatter.printJalviewFormat(sequences, featureColours,
- true, includeNonPositional);
+ includeNonPositional);
}
}
else
{
sf.addLink(link);
}
-
}
/**
- * generate a features file for seqs includes non-pos features by default.
- *
- * @param sequences
- * source of sequence features
- * @param visible
- * hash of feature types and colours
- * @return features file contents
- */
- public String printJalviewFormat(SequenceI[] sequences,
- Map<String, FeatureColourI> visible)
- {
- return printJalviewFormat(sequences, visible, true, true);
- }
-
- /**
- * generate a features file for seqs with colours from visible (if any)
+ * Returns contents of a Jalview format features file
*
* @param sequences
* source of features
* @param visible
- * hash of Colours for each feature type
- * @param visOnly
- * when true only feature types in 'visible' will be output
- * @param nonpos
- * indicates if non-positional features should be output (regardless
- * of group or type)
- * @return features file contents
+ * map of colour for each visible feature type
+ * @param includeNonPositional
+ * if true, include non-positional features (regardless of group or
+ * type)
+ * @return
*/
public String printJalviewFormat(SequenceI[] sequences,
- Map<String, FeatureColourI> visible, boolean visOnly,
- boolean nonpos)
+ Map<String, FeatureColourI> visible, boolean includeNonPositional)
{
- if (visOnly && !nonpos && (visible == null || visible.isEmpty()))
+ if (!includeNonPositional && (visible == null || visible.isEmpty()))
{
// no point continuing.
return "No Features Visible";
*/
// TODO: decide if feature links should also be written here ?
StringBuilder out = new StringBuilder(256);
- if (visible != null && visOnly) // todo why visOnly test?
+ if (visible != null)
{
for (Entry<String, FeatureColourI> featureColour : visible.entrySet())
{
// Work out which groups are both present and visible
Set<String> groups = new HashSet<String>();
- String[] types = visible == null ? null : visible.keySet().toArray(
- new String[visible.keySet().size()]);
+ String[] types = visible == null ? new String[0] : visible.keySet()
+ .toArray(new String[visible.keySet().size()]);
for (int i = 0; i < sequences.length; i++)
{
groups.addAll(sequences[i].getFeatures()
.getFeatureGroups(true, types));
- if (nonpos)
+ if (includeNonPositional)
{
groups.addAll(sequences[i].getFeatures().getFeatureGroups(false,
types));
for (int i = 0; i < sequences.length; i++)
{
List<SequenceFeature> features = new ArrayList<SequenceFeature>();
- if (nonpos)
+ if (includeNonPositional)
{
features.addAll(sequences[i].getFeatures().getFeaturesForGroup(
false, group, types));
}
- features.addAll(sequences[i].getFeatures().getFeaturesForGroup(
- true, group, types));
+ if (types.length > 0)
+ {
+ features.addAll(sequences[i].getFeatures().getFeaturesForGroup(
+ true, group, types));
+ }
for (SequenceFeature sequenceFeature : features)
{
}
/**
- * Returns features output in GFF2 format, including hidden and non-positional
- * features
- *
- * @param sequences
- * the sequences whose features are to be output
- * @param visible
- * a map whose keys are the type names of visible features
- * @return
- */
- public String printGffFormat(SequenceI[] sequences,
- Map<String, FeatureColourI> visible)
- {
- return printGffFormat(sequences, visible, true, true);
- }
-
- /**
* Returns features output in GFF2 format
*
* @param sequences
* the sequences whose features are to be output
* @param visible
* a map whose keys are the type names of visible features
- * @param outputVisibleOnly
* @param includeNonPositionalFeatures
* @return
*/
public String printGffFormat(SequenceI[] sequences,
- Map<String, FeatureColourI> visible, boolean outputVisibleOnly,
+ Map<String, FeatureColourI> visible,
boolean includeNonPositionalFeatures)
{
StringBuilder out = new StringBuilder(256);
*/
continue;
}
- // TODO why the test !isnonpos here?
- // what about not visible non-positional features?
- if (!isnonpos && outputVisibleOnly
- && !visible.containsKey(sf.type))
+ if (!isnonpos && !visible.containsKey(sf.type))
{
/*
* ignore not visible features if not wanted
assertFalse(iterator.hasNext());
/*
- * two types specified
+ * two types specified - get sorted alphabetically
*/
types = sf.varargToTypes("Metal", "Helix");
iterator = types.iterator();
assertTrue(iterator.hasNext());
- assertEquals(iterator.next(), "Metal");
- assertTrue(iterator.hasNext());
assertEquals(iterator.next(), "Helix");
+ assertTrue(iterator.hasNext());
+ assertEquals(iterator.next(), "Metal");
assertFalse(iterator.hasNext());
/*
types = sf.varargToTypes("Metal", null, "Helix");
iterator = types.iterator();
assertTrue(iterator.hasNext());
- assertEquals(iterator.next(), "Metal");
- assertTrue(iterator.hasNext());
assertEquals(iterator.next(), "Helix");
+ assertTrue(iterator.hasNext());
+ assertEquals(iterator.next(), "Metal");
assertFalse(iterator.hasNext());
}
FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
String exported = featuresFile.printJalviewFormat(
- al.getSequencesArray(), visible, true, false);
+ al.getSequencesArray(), visible, false);
String expected = "No Features Visible";
assertEquals(expected, exported);
/*
* include non-positional features
*/
- af.getViewport().setShowNPFeats(true);
exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
- visible, true, true);
+ visible, true);
expected = "\nSTARTGROUP\tuniprot\nCath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\nENDGROUP\tuniprot\n";
assertEquals(expected, exported);
/*
* set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
*/
- af.getViewport().setShowNPFeats(false);
fr.setVisible("METAL");
fr.setVisible("GAMMA-TURN");
visible = fr.getDisplayedFeatureCols();
exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
- visible, true, false);
+ visible, false);
expected = "METAL\tcc9900\n"
+ "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
+ "\nSTARTGROUP\tuniprot\n"
- + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ "ENDGROUP\tuniprot\n";
assertEquals(expected, exported);
fr.setVisible("Pfam");
visible = fr.getDisplayedFeatureCols();
exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
- visible, true, false);
+ visible, false);
/*
- * note the order of feature types is uncontrolled - derives from
- * FeaturesDisplayed.featuresDisplayed which is a HashSet
+ * features are output within group, ordered by sequence and by type
*/
expected = "METAL\tcc9900\n"
+ "Pfam\tff0000\n"
+ "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
+ "\nSTARTGROUP\tuniprot\n"
- + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
+ + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
+ "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
+ "ENDGROUP\tuniprot\n";
assertEquals(expected, exported);
git://source.jalview.org / jalview.git / commitdiff