/* Set up the CGView to display the plasmid */ private void initCgview() { int length = plasmid.getSequence().length(); cgview = new Cgview(length); // some optional settings cgview.setWidth(getWidth()); cgview.setHeight(getHeight()); cgview.setTitle(plasmid.getName()); cgview.setLabelPlacementQuality(100); cgview.setShowWarning(true); cgview.setLabelLineLength(8.0d); cgview.setLabelLineThickness(0.5f); cgview.setLabelShuffle(false); // create a FeatureSlot to hold sequence features FeatureSlot featureSlot = new FeatureSlot(cgview, CgviewConstants.DIRECT_STRAND); // create random sequence features List<org.autogene.core.bio.entities.Annotation> annotations = plasmid.getAnnotations(); HashMap<String, Integer> counts = new HashMap<String, Integer>(); // create the feature annotations to view in the plasmid for (int i = 0; i < annotations.size(); i++) { // update the label names such as Aapl (1) and Aapl (2) in the case that // there is more than one of the same annotation in two different locations Annotation a = annotations.get(i); String name = a.getFeature().getName(); int cur = 1; if (counts.containsKey(name)) { cur = counts.get(name); cur++; counts.put(name, cur); // Log.addText("plasmidpanel: " + name + "," + cur); } else { counts.put(name, cur); // Log.addText("plasmidpanel: " + name + "," + cur); } // simply create the feature System.out.println("ABCD creating feature with " + name + " " + cur); Feature feature = new Feature(featureSlot, (name + " (" + cur + ")")); feature.setColor( a.getScore() == 1.0 ? ColorConstants.NEUTRAL_COLOR_PERFECT_MATCH : ColorConstants.NEUTRAL_COLOR_IMPERFECT_MATCH); FeatureRange featureRange = new FeatureRange(feature, a.getStart(), a.getEnd()); } }
private void prepareToDraw() { if (forwardSlot0 != null) { forwardSlot0.setCgview(p); forwardSlot0.setFeatureThickness(featureThickness); } if (forwardSlot1 != null) { forwardSlot1.setCgview(p); forwardSlot1.setFeatureThickness(featureThickness); } if (forwardSlot2 != null) { forwardSlot2.setCgview(p); forwardSlot2.setFeatureThickness(featureThickness); } if (forwardSlot3 != null) { forwardSlot3.setCgview(p); forwardSlot3.setFeatureThickness(featureThickness); } if (forwardSlot4 != null) { forwardSlot4.setCgview(p); forwardSlot4.setFeatureThickness(featureThickness); } if (forwardSlot5 != null) { forwardSlot5.setCgview(p); forwardSlot5.setFeatureThickness(featureThickness); } if (forwardSlot6 != null) { forwardSlot6.setCgview(p); forwardSlot6.setFeatureThickness(featureThickness); } if (forwardSlot7 != null) { forwardSlot7.setCgview(p); forwardSlot7.setFeatureThickness(featureThickness); } if (reverseSlot0 != null) { reverseSlot0.setCgview(p); reverseSlot0.setFeatureThickness(featureThickness); } if (reverseSlot1 != null) { reverseSlot1.setCgview(p); reverseSlot1.setFeatureThickness(featureThickness); } if (reverseSlot2 != null) { reverseSlot2.setCgview(p); reverseSlot2.setFeatureThickness(featureThickness); } if (reverseSlot3 != null) { reverseSlot3.setCgview(p); reverseSlot3.setFeatureThickness(featureThickness); } if (reverseSlot4 != null) { reverseSlot4.setCgview(p); reverseSlot4.setFeatureThickness(featureThickness); } if (reverseSlot5 != null) { reverseSlot5.setCgview(p); reverseSlot5.setFeatureThickness(featureThickness); } if (reverseSlot6 != null) { reverseSlot6.setCgview(p); reverseSlot6.setFeatureThickness(featureThickness); } if (reverseSlot7 != null) { reverseSlot7.setCgview(p); reverseSlot7.setFeatureThickness(featureThickness); } if (restrictionSlot != null) { restrictionSlot.setCgview(p); restrictionSlot.setFeatureThickness(featureThickness); } // send settings to p if (showTitle) { p.setTitle(title); } p.setWidth(imageWidth); p.setHeight(imageHeight); p.setLabelsToKeep(MAXLABELS); p.setDrawTickMarks(drawTickMarks); p.setTitleFont(titleFont); p.setLabelFont(labelFont); p.setFeatureThickness(featureThickness); p.setBackboneThickness(backboneThickness); p.setFeatureSlotSpacing(featureSpacing); p.setLegendFont(legendFont); p.setTickLength(tickLength); p.setLabelLineLength(labelLineLength); p.setLabelPlacementQuality(labelPlacementQuality); p.setUseColoredLabelBackgrounds(useColoredLabelBackground); p.setShowBorder(showBorder); p.setShowShading(showShading); p.setShadingProportion(shadingProportion); p.setUseInnerLabels(useInnerLabels); p.setMoveInnerLabelsToOuter(moveInnerLabelsToOuter); p.setWarningFont(rulerFont); p.setRulerFont(rulerFont); // if not drawing labels, don't show message. if (!(showLabels)) { p.setShowWarning(false); } // set backboneRadius based on smallest image dimension int smallestDimension = Math.min(imageWidth, imageHeight); if (smallestDimension <= 750) { p.setBackboneRadius(0.50d * (double) smallestDimension / 2.0d); } else { p.setBackboneRadius(0.50d * 750.0d / 2.0d); } // check coloredLabels if (!(useColoredLabels)) { if (colorScheme == REGULAR) { p.setGlobalLabelColor((Color) MAP_ITEM_COLORS.get("titleFont")); } else if (colorScheme == INVERSE) { p.setGlobalLabelColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont")); } } // set map item colors if (colorScheme == REGULAR) { p.setLongTickColor((Color) MAP_ITEM_COLORS.get("tick")); p.setShortTickColor((Color) MAP_ITEM_COLORS.get("partialTick")); p.setZeroTickColor((Color) MAP_ITEM_COLORS.get("zeroLine")); p.setRulerFontColor((Color) MAP_ITEM_COLORS.get("rulerFont")); p.setBackboneColor((Color) MAP_ITEM_COLORS.get("backbone")); p.setTitleFontColor((Color) MAP_ITEM_COLORS.get("titleFont")); p.setWarningFontColor((Color) MAP_ITEM_COLORS.get("titleFont")); p.setBackgroundColor((Color) MAP_ITEM_COLORS.get("background")); } else if (colorScheme == INVERSE) { p.setLongTickColor((Color) MAP_ITEM_COLORS_INVERSE.get("tick")); p.setShortTickColor((Color) MAP_ITEM_COLORS_INVERSE.get("partialTick")); p.setZeroTickColor((Color) MAP_ITEM_COLORS_INVERSE.get("zeroLine")); p.setRulerFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("rulerFont")); p.setBackboneColor((Color) MAP_ITEM_COLORS_INVERSE.get("backbone")); p.setTitleFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont")); p.setWarningFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont")); p.setBackgroundColor((Color) MAP_ITEM_COLORS_INVERSE.get("background")); } // build legend if ((showLegend) && (DRAW_LEGEND_ITEMS.size() > 0)) { // create legend legend = new Legend(p); legend.setAllowLabelClash(allowLabelClashLegend); legend.setBackgroundOpacity(0.5f); legend.setFont(legendFont); legend.setPosition(legendPosition); if (colorScheme == REGULAR) { legend.setBackgroundColor((Color) MAP_ITEM_COLORS.get("background")); legend.setFontColor((Color) MAP_ITEM_COLORS.get("titleFont")); } else if (colorScheme == INVERSE) { legend.setBackgroundColor((Color) MAP_ITEM_COLORS_INVERSE.get("background")); legend.setFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont")); } LegendItem legendItem; Enumeration legendEntries = DRAW_LEGEND_ITEMS.keys(); ArrayList list = new ArrayList(); while (legendEntries.hasMoreElements()) { list.add(legendEntries.nextElement()); } Collections.sort(list); Iterator i = list.iterator(); while (i.hasNext()) { String key = (String) i.next(); legendItem = new LegendItem(legend); legendItem.setDrawSwatch(SWATCH_SHOW); legendItem.setLabel((String) LEGEND_ITEM_NAMES.get(key)); if (colorScheme == REGULAR) { legendItem.setSwatchColor((Color) FEATURE_COLORS.get(key)); } else if (colorScheme == INVERSE) { legendItem.setSwatchColor((Color) FEATURE_COLORS_INVERSE.get(key)); } } } // set message if (showMessage) { legend = new Legend(p); legend.setAllowLabelClash(false); legend.setBackgroundOpacity(0.5f); legend.setFont(messageFont); legend.setPosition(LEGEND_LOWER_RIGHT); LegendItem legendItem; if (colorScheme == REGULAR) { legend.setBackgroundColor((Color) MAP_ITEM_COLORS.get("background")); legend.setFontColor((Color) MAP_ITEM_COLORS.get("titleFont")); legendItem = new LegendItem(legend); legendItem.setLabel(message); legendItem.setDrawSwatch(SWATCH_NO_SHOW); } else if (colorScheme == INVERSE) { legend.setBackgroundColor((Color) MAP_ITEM_COLORS_INVERSE.get("background")); legend.setFontColor((Color) MAP_ITEM_COLORS_INVERSE.get("titleFont")); legendItem = new LegendItem(legend); legendItem.setLabel(message); legendItem.setDrawSwatch(SWATCH_NO_SHOW); } } }