+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param b DOCUMENT ME!\r
+ */\r
+ public void showSequenceFeatures(boolean b)\r
+ {\r
+ showSequenceFeatures = b;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
+ public void updateConservation()\r
+ {\r
+ Conservation cons = new jalview.analysis.Conservation("All",\r
+ jalview.schemes.ResidueProperties.propHash, 3,\r
+ alignment.getSequences(), 0, alignment.getWidth() - 1);\r
+ cons.calculate();\r
+ cons.verdict(false, ConsPercGaps);\r
+ cons.findQuality();\r
+\r
+ int alWidth = alignment.getWidth();\r
+ Annotation[] annotations = new Annotation[alWidth];\r
+ Annotation[] qannotations = new Annotation[alWidth];\r
+ String sequence = cons.getConsSequence().getSequence();\r
+ float minR;\r
+ float minG;\r
+ float minB;\r
+ float maxR;\r
+ float maxG;\r
+ float maxB;\r
+ minR = 0.3f;\r
+ minG = 0.0f;\r
+ minB = 0f;\r
+ maxR = 1.0f - minR;\r
+ maxG = 0.9f - minG;\r
+ maxB = 0f - minB; // scalable range for colouring both Conservation and Quality\r
+\r
+ float min = 0f;\r
+ float max = 11f;\r
+ float qmin = cons.qualityRange[0].floatValue();\r
+ float qmax = cons.qualityRange[1].floatValue();\r
+\r
+ for (int i = 0; i < alWidth; i++)\r
+ {\r
+ float value = 0;\r
+\r
+ try\r
+ {\r
+ value = Integer.parseInt(sequence.charAt(i) + "");\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ if (sequence.charAt(i) == '*')\r
+ {\r
+ value = 11;\r
+ }\r
+\r
+ if (sequence.charAt(i) == '+')\r
+ {\r
+ value = 10;\r
+ }\r
+ }\r
+\r
+ float vprop = value - min;\r
+ vprop /= max;\r
+ annotations[i] = new Annotation(sequence.charAt(i) + "",\r
+ String.valueOf(value), ' ', value,\r
+ new Color(minR + (maxR * vprop), minG + (maxG * vprop),\r
+ minB + (maxB * vprop)));\r
+\r
+ // Quality calc\r
+ value = ((Double) cons.quality.get(i)).floatValue();\r
+ vprop = value - qmin;\r
+ vprop /= qmax;\r
+ qannotations[i] = new Annotation(" ", String.valueOf(value), ' ',\r
+ value,\r
+ new Color(minR + (maxR * vprop), minG + (maxG * vprop),\r
+ minB + (maxB * vprop)));\r
+ }\r
+\r
+ if (conservation == null)\r
+ {\r
+ conservation = new AlignmentAnnotation("Conservation",\r
+ "Conservation of total alignment less than " +\r
+ ConsPercGaps + "% gaps", annotations, 0f, // cons.qualityRange[0].floatValue(),\r
+ 11f, // cons.qualityRange[1].floatValue()\r
+ 1);\r
+\r
+ if (showConservation)\r
+ {\r
+ alignment.addAnnotation(conservation);\r
+ }\r
+\r
+ quality = new AlignmentAnnotation("Quality",\r
+ "Alignment Quality based on Blosum62 scores", qannotations,\r
+ cons.qualityRange[0].floatValue(),\r
+ cons.qualityRange[1].floatValue(), 1);\r
+\r
+ if (showQuality)\r
+ {\r
+ alignment.addAnnotation(quality);\r
+ }\r
+ }\r
+ 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 = Float.parseFloat(hash.get("maxCount").toString());\r
+ value /= Float.parseFloat(hash.get("size").toString());\r
+\r
+ value *= 100;\r
+\r
+ String maxRes = hash.get("maxResidue") + " ";\r
+ String mouseOver = hash.get("maxResidue") + " ";\r
+\r
+ if (maxRes.length() > 2)\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
+\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
+ javax.swing.JFrame temp = new javax.swing.JFrame();\r
+ temp.addNotify();\r
+\r
+ java.awt.FontMetrics fm = temp.getGraphics().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