int startSeq;\r
int endSeq;\r
\r
- boolean showFullId = true;\r
+ boolean showJVSuffix = true;\r
boolean showText = true;\r
boolean showColourText = false;\r
boolean showBoxes = true;\r
\r
int charHeight;\r
int charWidth;\r
- int chunkWidth;\r
- int chunkHeight;\r
+ int wrappedWidth;\r
\r
Font font = new Font("SansSerif", Font.PLAIN, 10);\r
AlignmentI alignment;\r
boolean scaleLeftWrapped = true;\r
boolean scaleRightWrapped = true;\r
\r
+ // The following vector holds the features which are\r
+ // currently visible, in the correct order or rendering\r
+ Hashtable featuresDisplayed = null;\r
+\r
+\r
public Vector vconsensus;\r
AlignmentAnnotation consensus;\r
AlignmentAnnotation conservation;\r
String param = applet.getParameter("showFullId");\r
if (param != null)\r
{\r
- showFullId = Boolean.valueOf(param).booleanValue();\r
+ showJVSuffix = Boolean.valueOf(param).booleanValue();\r
}\r
\r
param = applet.getParameter("showAnnotation");\r
annotations,\r
0f, // cons.qualityRange[0].floatValue(),\r
11f, // cons.qualityRange[1].floatValue()\r
- 1);\r
+ AlignmentAnnotation.BAR_GRAPH);\r
if (showConservation)\r
{\r
alignment.addAnnotation(conservation);\r
qannotations,\r
cons.qualityRange[0].floatValue(),\r
cons.qualityRange[1].floatValue(),\r
- 1);\r
+ AlignmentAnnotation.BAR_GRAPH);\r
if (showQuality)\r
{\r
alignment.addAnnotation(quality);\r
if (consensus == null)\r
{\r
consensus = new AlignmentAnnotation("Consensus",\r
- "PID", annotations, 0f, 100f, 1);\r
+ "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);\r
if (showConsensus)\r
{\r
alignment.addAnnotation(consensus);\r
return charHeight;\r
}\r
\r
- public void setChunkWidth(int w)\r
- {\r
- this.chunkWidth = w;\r
- }\r
-\r
- public int getChunkWidth()\r
- {\r
- return chunkWidth;\r
- }\r
-\r
- public void setChunkHeight(int h)\r
+ public void setWrappedWidth(int w)\r
{\r
- this.chunkHeight = h;\r
+ this.wrappedWidth = w;\r
}\r
\r
- public int getChunkHeight()\r
+ public int getwrappedWidth()\r
{\r
- return chunkHeight;\r
+ return wrappedWidth;\r
}\r
\r
public AlignmentI getAlignment()\r
return colourAppliesToAllGroups;\r
}\r
\r
- public boolean getShowFullId()\r
+ public boolean getShowJVSuffix()\r
{\r
- return showFullId;\r
+ return showJVSuffix;\r
}\r
\r
- public void setShowFullId(boolean b)\r
+ public void setShowJVSuffix(boolean b)\r
{\r
- showFullId = b;\r
+ showJVSuffix = b;\r
}\r
\r
public boolean getShowAnnotation()\r