import jalview.api.AlignmentViewPanel;
import jalview.api.ComplexAlignFile;
import jalview.api.FeatureRenderer;
+import jalview.api.FeatureSettingsModelI;
import jalview.api.FeaturesDisplayedI;
import jalview.bin.BuildDetails;
import jalview.datamodel.AlignmentAnnotation;
AnnotationDisplaySettingPojo annotSetting = new AnnotationDisplaySettingPojo();
annotSetting.setBelowAlignment(annot.belowAlignment);
annotSetting.setCentreColLabels(annot.centreColLabels);
- annotSetting.setScaleColLabel(annot.centreColLabels);
+ annotSetting.setScaleColLabel(annot.scaleColLabel);
annotSetting.setShowAllColLabels(annot.showAllColLabels);
annotSetting.setVisible(annot.visible);
+ annotSetting.setHasIcon(annot.hasIcons);
alignAnnotPojo.setAnnotationSettings(annotSetting);
SequenceI refSeq = annot.sequenceRef;
if (refSeq != null)
annotationPojo.setValue(annotation.value);
annotationPojo
.setSecondaryStructure(annotation.secondaryStructure);
- annotationPojo.setDisplayCharacter(annotation.displayCharacter);
+ String displayChar = annotation.displayCharacter == null ? null
+ : annotation.displayCharacter;
+ // System.out.println("--------------------->[" + displayChar + "]");
+ annotationPojo.setDisplayCharacter(displayChar);
if (annotation.colour != null)
{
annotationPojo.setColour(jalview.util.Format
seqMap.put(seqUniqueId, seq);
}
-
parseFeatures(jsonSeqArray);
for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
}
}
SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
- displayBoxes, displayText, colourText,
- startRes, endRes);
+ displayBoxes, displayText, colourText, startRes, endRes);
seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
seqGrp);
seqGrp.setShowNonconserved(showNonconserved);
.get("secondaryStructure").toString().charAt(0);
String displayChar = annot.get("displayCharacter") == null ? ""
: annot.get("displayCharacter").toString();
- Color color = annot.get("colour") == null ? Color.white
- : UserColourScheme.getColourFromString(annot.get(
- "colour").toString());
- annotations[count] = new Annotation(displayChar, desc, ss, val,
- color);
+
+ annotations[count] = new Annotation(displayChar, desc, ss, val);
+ if (annot.get("colour") != null)
+ {
+ Color color = UserColourScheme.getColourFromString(annot.get(
+ "colour").toString());
+ annotations[count].colour = color;
+ }
}
++count;
}
.get("label").toString(), alAnnot.get("description")
.toString(), annotations);
alignAnnot.graph = (alAnnot.get("graphType") == null) ? 0 : Integer
- .valueOf(alAnnot.get("graphType")
- .toString());
+ .valueOf(alAnnot.get("graphType").toString());
JSONObject diplaySettings = (JSONObject) alAnnot
.get("annotationSettings");
alignAnnot.visible = (diplaySettings.get("visible") == null) ? true
: Boolean.valueOf(diplaySettings.get("visible")
.toString());
+ alignAnnot.hasIcons = (diplaySettings.get("hasIcon") == null) ? true
+ : Boolean.valueOf(diplaySettings.get("hasIcon")
+ .toString());
}
if (alAnnot.get("score") != null)
alignAnnot.adjustForAlignment();
}
}
+ alignAnnot.validateRangeAndDisplay();
this.annotations.add(alignAnnot);
+
}
} catch (Exception e)
{
}
}
+ @Override
public String getGlobalColourScheme()
{
return globalColourScheme;
this.displayedFeatures = displayedFeatures;
}
+ @Override
public void configureForView(AlignmentViewPanel avpanel)
{
+ if (avpanel == null)
+ {
+ return;
+ }
super.configureForView(avpanel);
AlignViewportI viewport = avpanel.getAlignViewport();
AlignmentI alignment = viewport.getAlignment();
fr = avpanel.cloneFeatureRenderer();
// Add non auto calculated annotation to AlignFile
- for (AlignmentAnnotation annot : annots)
+ if (annots != null)
{
- if (annot != null && !annot.autoCalculated)
+ for (AlignmentAnnotation annot : annots)
{
- annotations.add(annot);
+ if (annot != null && !annot.autoCalculated)
+ {
+ annotations.add(annot);
+ }
}
}
globalColourScheme = ColourSchemeProperty.getColourName(viewport
}
+ @Override
public boolean isShowSeqFeatures()
{
return showSeqFeatures;
return hiddenColumns;
}
+ @Override
public ColumnSelection getColumnSelection()
{
return columnSelection;
this.columnSelection = columnSelection;
}
+ @Override
public SequenceI[] getHiddenSequences()
{
if (hiddenSequences == null || hiddenSequences.isEmpty())
this.exportJalviewSettings = exportJalviewSettings;
}
}
+
+ /**
+ * Returns a descriptor for suitable feature display settings with
+ * <ul>
+ * <li>ResNums or insertions features visible</li>
+ * <li>insertions features coloured red</li>
+ * <li>ResNum features coloured by label</li>
+ * <li>Insertions displayed above (on top of) ResNums</li>
+ * </ul>
+ */
+ @Override
+ public FeatureSettingsModelI getFeatureColourScheme()
+ {
+ return new PDBFeatureSettings();
+ }
}