+ else\r
+ {\r
+ conservation.annotations = annotations;\r
+ quality.annotations = qannotations;\r
+ quality.graphMax = cons.qualityRange[1].floatValue();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void updateConsensus()\r
+ {\r
+ Annotation[] annotations = new Annotation[alignment.getWidth()];\r
+\r
+ // this routine prevents vconsensus becoming a new object each time\r
+ // consenus is calculated. Important for speed of Blosum62\r
+ // and PID colouring of alignment\r
+ if (vconsensus == null)\r
+ {\r
+ vconsensus = alignment.getAAFrequency();\r
+ }\r
+ else\r
+ {\r
+ Vector temp = alignment.getAAFrequency();\r
+ vconsensus.clear();\r
+\r
+ Enumeration e = temp.elements();\r
+\r
+ while (e.hasMoreElements())\r
+ {\r
+ vconsensus.add(e.nextElement());\r
+ }\r
+ }\r
+\r
+ Hashtable hash = null;\r
+\r
+ for (int i = 0; i < alignment.getWidth(); i++)\r
+ {\r
+ hash = (Hashtable) vconsensus.elementAt(i);\r
+\r
+ float value = 0;\r
+ if(ignoreGapsInConsensusCalculation)\r
+ value = ((Float)hash.get("pid_nogaps")).floatValue();\r
+ else\r
+ value = ((Float)hash.get("pid_gaps")).floatValue();\r
+\r
+ String maxRes = hash.get("maxResidue").toString();\r
+ String mouseOver = hash.get("maxResidue")+" ";\r
+\r
+ if (maxRes.length() > 1)\r
+ {\r
+ mouseOver = "[" + maxRes + "] ";\r
+ maxRes = "+";\r
+ }\r
+\r
+ mouseOver += ((int) value + "%");\r
+ annotations[i] = new Annotation(maxRes, mouseOver, ' ', value);\r
+ }\r
+\r
+ if (consensus == null)\r
+ {\r
+ consensus = new AlignmentAnnotation("Consensus", "PID",\r
+ annotations, 0f, 100f, 1);\r
+\r
+ if (showIdentity)\r
+ {\r
+ alignment.addAnnotation(consensus);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ consensus.annotations = annotations;\r
+ }\r
+\r
+ if(globalColourScheme!=null)\r
+ globalColourScheme.setConsensus(vconsensus);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public SequenceGroup getSelectionGroup()\r
+ {\r
+ return selectionGroup;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param sg DOCUMENT ME!\r
+ */\r
+ public void setSelectionGroup(SequenceGroup sg)\r
+ {\r
+ selectionGroup = sg;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getConservationSelected()\r
+ {\r
+ return conservationColourSelected;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param b DOCUMENT ME!\r
+ */\r
+ public void setConservationSelected(boolean b)\r
+ {\r
+ conservationColourSelected = b;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public boolean getAbovePIDThreshold()\r
+ {\r
+ return abovePIDThreshold;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param b DOCUMENT ME!\r
+ */\r
+ public void setAbovePIDThreshold(boolean b)\r
+ {\r
+ abovePIDThreshold = b;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getStartRes()\r
+ {\r
+ return startRes;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getEndRes()\r
+ {\r
+ return endRes;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getStartSeq()\r
+ {\r
+ return startSeq;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param cs DOCUMENT ME!\r
+ */\r
+ public void setGlobalColourScheme(ColourSchemeI cs)\r
+ {\r
+ globalColourScheme = cs;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public ColourSchemeI getGlobalColourScheme()\r
+ {\r
+ return globalColourScheme;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param res DOCUMENT ME!\r
+ */\r
+ public void setStartRes(int res)\r
+ {\r
+ this.startRes = res;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param seq DOCUMENT ME!\r
+ */\r
+ public void setStartSeq(int seq)\r
+ {\r
+ this.startSeq = seq;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param res DOCUMENT ME!\r
+ */\r
+ public void setEndRes(int res)\r
+ {\r
+ if (res > (alignment.getWidth() - 1))\r
+ {\r
+ // log.System.out.println(" Corrected res from " + res + " to maximum " + (alignment.getWidth()-1));\r
+ res = alignment.getWidth() - 1;\r
+ }\r
+\r
+ if (res < 0)\r
+ {\r
+ res = 0;\r
+ }\r
+\r
+ this.endRes = res;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param seq DOCUMENT ME!\r
+ */\r
+ public void setEndSeq(int seq)\r
+ {\r
+ if (seq > alignment.getHeight())\r
+ {\r
+ seq = alignment.getHeight();\r
+ }\r
+\r
+ if (seq < 0)\r
+ {\r
+ seq = 0;\r
+ }\r
+\r
+ this.endSeq = seq;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getEndSeq()\r
+ {\r
+ return endSeq;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param f DOCUMENT ME!\r
+ */\r
+ public void setFont(Font f)\r
+ {\r
+ font = f;\r
+\r
+ Container c = new Container();\r
+\r
+ java.awt.FontMetrics fm = c.getFontMetrics(font);\r
+ setCharHeight(fm.getHeight());\r
+ setCharWidth(fm.charWidth('M'));\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public Font getFont()\r
+ {\r
+ return font;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param w DOCUMENT ME!\r
+ */\r
+ public void setCharWidth(int w)\r
+ {\r
+ this.charWidth = w;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getCharWidth()\r
+ {\r
+ return charWidth;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param h DOCUMENT ME!\r
+ */\r
+ public void setCharHeight(int h)\r
+ {\r
+ this.charHeight = h;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getCharHeight()\r
+ {\r
+ return charHeight;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param w DOCUMENT ME!\r
+ */\r
+ public void setChunkWidth(int w)\r
+ {\r
+ this.chunkWidth = w;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @return DOCUMENT ME!\r
+ */\r
+ public int getChunkWidth()\r
+ {\r
+ return chunkWidth;\r