- int startRes;\r
- int endRes;\r
-\r
- int startSeq;\r
- int endSeq;\r
-\r
- boolean showFullId = false;\r
- boolean showText=true;\r
- boolean showColourText=false;\r
- boolean showBoxes=true;\r
- boolean wrapAlignment=false;\r
- boolean renderGaps = true;\r
- boolean showSequenceFeatures = false;\r
-\r
- boolean colourAppliesToAllGroups = true;\r
- ColourSchemeI globalColourScheme = null;\r
- boolean conservationColourSelected = false;\r
- boolean abovePIDThreshold = false;\r
-\r
- SequenceGroup selectionGroup = new SequenceGroup();\r
-\r
- RendererI renderer = new SequenceRenderer(this);\r
-\r
- int charHeight;\r
- int charWidth;\r
- int chunkWidth;\r
- int chunkHeight;\r
-\r
- Font font = new Font("SansSerif",Font.PLAIN,10);\r
- AlignmentI alignment;\r
-\r
- ColumnSelection colSel = new ColumnSelection();\r
-\r
- String visibleConsensus;\r
-\r
- int threshold;\r
- int increment;\r
-\r
- NJTree currentTree = null;\r
-\r
-\r
- public AlignViewport(AlignmentI da,\r
- boolean showText,\r
- boolean showBoxes,\r
- boolean wrapAlignment) {\r
- this(0,da.getWidth()-1,0,da.getHeight()-1,\r
- showText,\r
- showBoxes,\r
- wrapAlignment);\r
-\r
- setAlignment(da);\r
- }\r
-\r
- public AlignViewport(int startRes, int endRes,\r
- int startSeq, int endSeq,\r
- boolean showText,\r
- boolean showBoxes,\r
- boolean wrapAlignment) {\r
-\r
- this.startRes = startRes;\r
- this.endRes = endRes;\r
- this.startSeq = startSeq;\r
- this.endSeq = endSeq;\r
- this.showText = showText;\r
- this.showBoxes = showBoxes;\r
- this.wrapAlignment = wrapAlignment;\r
-\r
- setFont( font );\r
- }\r
-\r
- public void showSequenceFeatures(boolean b)\r
- {\r
- showSequenceFeatures = b;\r
- }\r
-\r
- public String getVisibleConsensus()\r
- {\r
- return visibleConsensus;\r
- }\r
-\r
- Vector consensus = new Vector();\r
- public Vector getConsensus(boolean recalculate)\r
- {\r
- if(recalculate || consensus.size()<1)\r
- {\r
- consensus = alignment.getAAFrequency();\r
- StringBuffer sb = new StringBuffer();\r
- Hashtable hash = null;\r
- for (int i = 0; i < consensus.size(); i++)\r
+ int startRes;\r
+ int endRes;\r
+ int startSeq;\r
+ int endSeq;\r
+ boolean showJVSuffix = true;\r
+ boolean showText = true;\r
+ boolean showColourText = false;\r
+ boolean showBoxes = true;\r
+ boolean wrapAlignment = false;\r
+ boolean renderGaps = true;\r
+ boolean showSequenceFeatures = false;\r
+ boolean showAnnotation = true;\r
+ boolean showConservation = true;\r
+ boolean showQuality = true;\r
+ boolean showIdentity = true;\r
+ boolean colourAppliesToAllGroups = true;\r
+ ColourSchemeI globalColourScheme = null;\r
+ boolean conservationColourSelected = false;\r
+ boolean abovePIDThreshold = false;\r
+ SequenceGroup selectionGroup;\r
+ int charHeight;\r
+ int charWidth;\r
+ int wrappedWidth;\r
+ Font font = new Font("SansSerif", Font.PLAIN, 10);\r
+ AlignmentI alignment;\r
+ ColumnSelection colSel = new ColumnSelection();\r
+ int threshold;\r
+ int increment;\r
+ NJTree currentTree = null;\r
+ boolean scaleAboveWrapped = false;\r
+ boolean scaleLeftWrapped = true;\r
+ boolean scaleRightWrapped = true;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public Vector vconsensus;\r
+ AlignmentAnnotation consensus;\r
+ AlignmentAnnotation conservation;\r
+ AlignmentAnnotation quality;\r
+\r
+ /** DOCUMENT ME!! */\r
+ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
+\r
+ // JBPNote Prolly only need this in the applet version.\r
+ private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);\r
+\r
+ boolean ignoreGapsInConsensusCalculation = false;\r
+\r
+ boolean isDataset = false;\r
+\r
+\r
+ public AlignViewport(AlignmentI al, boolean dataset)\r
+ {\r
+ isDataset = dataset;\r
+ setAlignment(al);\r
+ init();\r
+ }\r
+ /**\r
+ * Creates a new AlignViewport object.\r
+ *\r
+ * @param al DOCUMENT ME!\r
+ */\r
+ public AlignViewport(AlignmentI al)\r
+ {\r
+ setAlignment(al);\r
+ init();\r
+ }\r
+\r
+ void init()\r
+ {\r
+ this.startRes = 0;\r
+ this.endRes = alignment.getWidth() - 1;\r
+ this.startSeq = 0;\r
+ this.endSeq = alignment.getHeight() - 1;\r
+\r
+ showJVSuffix = Cache.getDefault("SHOW_JVSUFFIX", true);\r
+ showAnnotation = Cache.getDefault("SHOW_ANNOTATIONS", true);\r
+ showConservation = Cache.getDefault("SHOW_CONSERVATION", true);\r
+\r
+ showQuality = Cache.getDefault("SHOW_QUALITY", true);\r
+ showIdentity = Cache.getDefault("SHOW_IDENTITY", true);\r
+\r
+ String fontName = Cache.getDefault("FONT_NAME", "SansSerif");\r
+ String fontStyle = Cache.getDefault("FONT_STYLE", Font.PLAIN + "") ;\r
+ String fontSize = Cache.getDefault("FONT_SIZE", "10");\r
+\r
+ int style = 0;\r
+\r
+ if (fontStyle.equals("bold"))\r
+ {\r
+ style = 1;\r
+ }\r
+ else if (fontStyle.equals("italic"))\r
+ {\r
+ style = 2;\r
+ }\r
+\r
+ setFont(new Font(fontName, style, Integer.parseInt(fontSize)));\r
+\r
+\r
+ alignment.setGapCharacter( Cache.getDefault("GAP_SYMBOL", "-").charAt(0) );\r
+\r
+\r
+ // We must set conservation and consensus before setting colour,\r
+ // as Blosum and Clustal require this to be done\r
+ if(vconsensus==null && !isDataset)\r
+ {\r
+ updateConservation();\r
+ updateConsensus();\r
+ }\r
+\r
+ if (jalview.bin.Cache.getProperty("DEFAULT_COLOUR") != null)\r
+ {\r
+ globalColourScheme = ColourSchemeProperty.getColour(alignment,\r
+ jalview.bin.Cache.getProperty("DEFAULT_COLOUR"));\r
+\r
+ if (globalColourScheme instanceof UserColourScheme)\r
+ {\r
+ globalColourScheme = UserDefinedColours.loadDefaultColours();\r
+ ((UserColourScheme)globalColourScheme).setThreshold(0, getIgnoreGapsConsensus());\r
+ }\r
+\r
+ if (globalColourScheme != null)\r
+ {\r
+ globalColourScheme.setConsensus(vconsensus);\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+\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
+ if(alignment.isNucleotide())\r
+ return;\r
+\r
+ try{\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),\r
+ 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),\r
+ 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",\r
+ 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",\r
+ qannotations,\r
+ cons.qualityRange[0].floatValue(),\r
+ cons.qualityRange[1].floatValue(),\r
+ 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
+ catch (OutOfMemoryError error)\r