import jalview.analysis.SequenceIdMatcher;
import jalview.api.AlignViewportI;
import jalview.api.FeatureColourI;
+import jalview.api.FeatureRenderer;
import jalview.api.FeaturesSourceI;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
}
/**
- * Returns contents of a Jalview format features file, for visible features, as
- * filtered by type and group. Features with a null group are displayed if their
- * feature type is visible. Non-positional features may optionally be included
- * (with no check on type or group).
+ * Returns contents of a Jalview format features file, for visible features,
+ * as filtered by type and group. Features with a null group are displayed if
+ * their feature type is visible. Non-positional features may optionally be
+ * included (with no check on type or group).
*
* @param sequences
- * source of features
- * @param visible
- * map of colour for each visible feature type
- * @param featureFilters
- * @param visibleFeatureGroups
+ * @param fr
* @param includeNonPositional
* if true, include non-positional features (regardless of group or
* type)
* @return
*/
public String printJalviewFormat(SequenceI[] sequences,
- Map<String, FeatureColourI> visible,
- Map<String, FeatureMatcherSetI> featureFilters,
- List<String> visibleFeatureGroups, boolean includeNonPositional)
+ FeatureRenderer fr, boolean includeNonPositional)
{
- if (!includeNonPositional && (visible == null || visible.isEmpty()))
+ Map<String, FeatureColourI> visibleColours = fr
+ .getDisplayedFeatureCols();
+ Map<String, FeatureMatcherSetI> featureFilters = fr.getFeatureFilters();
+ List<String> visibleFeatureGroups = fr.getDisplayedFeatureGroups();
+
+ if (!includeNonPositional
+ && (visibleColours == null || visibleColours.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)
+ if (visibleColours != null)
{
- for (Entry<String, FeatureColourI> featureColour : visible.entrySet())
+ for (Entry<String, FeatureColourI> featureColour : visibleColours
+ .entrySet())
{
FeatureColourI colour = featureColour.getValue();
out.append(colour.toJalviewFormat(featureColour.getKey())).append(
}
}
- String[] types = visible == null ? new String[0] : visible.keySet()
- .toArray(new String[visible.keySet().size()]);
+ String[] types = visibleColours == null ? new String[0]
+ : visibleColours.keySet()
+ .toArray(new String[visibleColours.keySet().size()]);
/*
* feature filters if any
*/
- outputFeatureFilters(out, visible, featureFilters);
+ outputFeatureFilters(out, visibleColours, featureFilters);
/*
* sort groups alphabetically, and ensure that features with a
/*
* positional features within groups
*/
- foundSome |= outputFeaturesByGroup(out, sortedGroups, types, sequences);
+ foundSome |= outputFeaturesByGroup(out, fr, sortedGroups, types,
+ sequences);
return foundSome ? out.toString() : "No Features Visible";
}
}
if (!first)
{
- out.append(ENDFILTERS).append(newline).append(newline);
+ out.append(ENDFILTERS).append(newline);
}
}
/**
- * Appends output of sequence features within feature groups to the output
- * buffer. Groups other than the null or empty group are sandwiched by
- * STARTGROUP and ENDGROUP lines.
+ * Appends output of visible sequence features within feature groups to the
+ * output buffer. Groups other than the null or empty group are sandwiched by
+ * STARTGROUP and ENDGROUP lines. Answers true if at least one feature was
+ * written, else false.
*
* @param out
+ * @param fr
* @param groups
* @param featureTypes
* @param sequences
* @return
*/
private boolean outputFeaturesByGroup(StringBuilder out,
- List<String> groups, String[] featureTypes, SequenceI[] sequences)
+ FeatureRenderer fr, List<String> groups, String[] featureTypes,
+ SequenceI[] sequences)
{
boolean foundSome = false;
for (String group : groups)
{
+ boolean firstInGroup = true;
boolean isNamedGroup = (group != null && !"".equals(group));
- if (isNamedGroup)
- {
- out.append(newline);
- out.append(STARTGROUP).append(TAB);
- out.append(group);
- out.append(newline);
- }
/*
* output positional features within groups
for (SequenceFeature sequenceFeature : features)
{
- foundSome = true;
- out.append(formatJalviewFeature(sequenceName, sequenceFeature));
+ if (fr.isVisible(sequenceFeature))
+ {
+ foundSome = true;
+ if (firstInGroup && isNamedGroup)
+ {
+ out.append(newline).append(STARTGROUP).append(TAB)
+ .append(group).append(newline);
+ }
+ firstInGroup = false;
+ out.append(formatJalviewFeature(sequenceName, sequenceFeature));
+ }
}
}
- if (isNamedGroup)
+ if (isNamedGroup && !firstInGroup)
{
- out.append(ENDGROUP).append(TAB);
- out.append(group);
- out.append(newline);
+ out.append(ENDGROUP).append(TAB).append(group).append(newline);
}
}
return foundSome;
* @return
*/
public String printGffFormat(SequenceI[] sequences,
- Map<String, FeatureColourI> visible,
- List<String> visibleFeatureGroups,
- boolean includeNonPositionalFeatures)
+ FeatureRenderer fr, boolean includeNonPositionalFeatures)
{
+ Map<String, FeatureColourI> visibleColours = fr.getDisplayedFeatureCols();
+
StringBuilder out = new StringBuilder(256);
out.append(String.format("%s %d\n", GFF_VERSION, gffVersion == 0 ? 2 : gffVersion));
if (!includeNonPositionalFeatures
- && (visible == null || visible.isEmpty()))
+ && (visibleColours == null || visibleColours.isEmpty()))
{
return out.toString();
}
- String[] types = visible == null ? new String[0] : visible.keySet()
- .toArray(
- new String[visible.keySet().size()]);
+ String[] types = visibleColours == null ? new String[0]
+ : visibleColours.keySet()
+ .toArray(new String[visibleColours.keySet().size()]);
for (SequenceI seq : sequences)
{
{
features.addAll(seq.getFeatures().getNonPositionalFeatures());
}
- if (visible != null && !visible.isEmpty())
+ if (visibleColours != null && !visibleColours.isEmpty())
{
features.addAll(seq.getFeatures().getPositionalFeatures(types));
}
for (SequenceFeature sf : features)
{
- String source = sf.featureGroup;
- if (!sf.isNonPositional() && source != null
- && !visibleFeatureGroups.contains(source))
+ if (!sf.isNonPositional() && !fr.isVisible(sf))
{
- // group is not visible
+ /*
+ * feature hidden by group visibility, colour threshold,
+ * or feature filter condition
+ */
continue;
}
+ String source = sf.featureGroup;
if (source == null)
{
source = sf.getDescription();
git://source.jalview.org / jalview.git / blobdiff