+ av.featuresDisplayed = new Hashtable();\r
+ }\r
+\r
+ if (featureGroups == null)\r
+ {\r
+ featureGroups = new Hashtable();\r
+ }\r
+\r
+ col = colourPanel.getBackground();\r
+ setColour(lastFeatureAdded, col);\r
+\r
+ if(lastFeatureGroupAdded!=null)\r
+ {\r
+ featureGroups.put(lastFeatureGroupAdded, new Boolean(true));\r
+ av.featuresDisplayed.put(lastFeatureGroupAdded,\r
+ new Integer(col.getRGB()));\r
+ }\r
+ findAllFeatures();\r
+\r
+ String [] tro = new String[renderOrder.length];\r
+ tro[0] = renderOrder[renderOrder.length-1];\r
+ System.arraycopy(renderOrder,0,tro,1,renderOrder.length-1);\r
+ renderOrder = tro;\r
+\r
+ ap.paintAlignment(true);\r
+\r
+ return true;\r
+ }\r
+ else\r
+ {\r
+ return false;\r
+ }\r
+ }\r
+\r
+ findAllFeatures();\r
+\r
+ ap.paintAlignment(true);\r
+\r
+ return true;\r
+ }\r
+\r
+\r
+ public Color findFeatureColour(Color initialCol, SequenceI seq, int i)\r
+ {\r
+ overview = true;\r
+ if (!av.showSequenceFeatures)\r
+ {\r
+ return initialCol;\r
+ }\r
+\r
+ lastSeq = seq;\r
+ sequenceFeatures = lastSeq.getSequenceFeatures();\r
+ if (sequenceFeatures == null)\r
+ {\r
+ return initialCol;\r
+ }\r
+\r
+ sfSize = sequenceFeatures.length;\r
+\r
+ if (jalview.util.Comparison.isGap(lastSeq.getCharAt(i)))\r
+ {\r
+ return Color.white;\r
+ }\r
+\r
+ currentColour = null;\r
+\r
+ drawSequence(null, lastSeq, lastSeq.findPosition(i), -1, -1);\r
+\r
+ if (currentColour == null)\r
+ {\r
+ return initialCol;\r
+ }\r
+\r
+ return new Color( ( (Integer) currentColour).intValue());\r
+ }\r
+\r
+ /**\r
+ * This is used by the Molecule Viewer to get the accurate colour\r
+ * of the rendered sequence\r
+ */\r
+ boolean overview = false;\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param g DOCUMENT ME!\r
+ * @param seq DOCUMENT ME!\r
+ * @param sg DOCUMENT ME!\r
+ * @param start DOCUMENT ME!\r
+ * @param end DOCUMENT ME!\r
+ * @param x1 DOCUMENT ME!\r
+ * @param y1 DOCUMENT ME!\r
+ * @param width DOCUMENT ME!\r
+ * @param height DOCUMENT ME!\r
+ */\r
+ // String type;\r
+ // SequenceFeature sf;\r
+\r
+ SequenceI lastSeq;\r
+ SequenceFeature[] sequenceFeatures;\r
+ int sfSize, sfindex, spos, epos;\r
+\r
+ synchronized public void drawSequence(Graphics g, SequenceI seq,\r
+ int start, int end, int y1)\r
+ {\r
+ if (seq.getSequenceFeatures() == null\r
+ || seq.getSequenceFeatures().length == 0)\r
+ {\r
+ return;\r
+ }\r
+\r
+ if (transparencySetter != null && g != null)\r
+ {\r
+ transparencySetter.setTransparency(g, transparency);\r
+ }\r
+\r
+ if (lastSeq == null || seq != lastSeq || sequenceFeatures!=seq.getSequenceFeatures())\r
+ {\r
+ lastSeq = seq;\r
+ sequenceFeatures = seq.getSequenceFeatures();\r
+ sfSize = sequenceFeatures.length;\r
+ }\r
+\r
+ if (av.featuresDisplayed == null || renderOrder == null)\r
+ {\r
+ findAllFeatures();\r
+ if (av.featuresDisplayed.size() < 1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ sequenceFeatures = seq.getSequenceFeatures();\r
+ sfSize = sequenceFeatures.length;\r
+ }\r
+ if (!overview)\r
+ {\r
+ spos = lastSeq.findPosition(start);\r
+ epos = lastSeq.findPosition(end);\r
+ if (g != null)\r
+ {\r
+ fm = g.getFontMetrics();\r
+ }\r
+ }\r
+ String type;\r
+ for (int renderIndex = 0; renderIndex < renderOrder.length; renderIndex++)\r
+ {\r
+ type = renderOrder[renderIndex];\r
+ if (!av.featuresDisplayed.containsKey(type))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ // loop through all features in sequence to find\r
+ // current feature to render\r
+ for (sfindex = 0; sfindex < sfSize; sfindex++)\r
+ {\r
+ if (!sequenceFeatures[sfindex].type.equals(type))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (featureGroups != null\r
+ && sequenceFeatures[sfindex].featureGroup != null\r
+ &&\r
+ featureGroups.containsKey(sequenceFeatures[sfindex].featureGroup)\r
+ &&\r
+ ! ( (Boolean) featureGroups.get(sequenceFeatures[sfindex].\r
+ featureGroup)).\r
+ booleanValue())\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (!overview && (sequenceFeatures[sfindex].getBegin() > epos\r
+ || sequenceFeatures[sfindex].getEnd() < spos))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ if (overview)\r
+ {\r
+ if (sequenceFeatures[sfindex].begin <= start &&\r
+ sequenceFeatures[sfindex].end >= start)\r