int startSeq;\r
int endSeq;\r
\r
+\r
+ boolean cursorMode = false;\r
+\r
boolean showJVSuffix = true;\r
boolean showText = true;\r
boolean showColourText = false;\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
AlignmentAnnotation quality;\r
\r
+ boolean autocalculateConsensus = true;\r
+\r
public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
\r
private java.beans.PropertyChangeSupport changeSupport = new java.beans.PropertyChangeSupport(this);\r
showSequenceFeatures = b;\r
}\r
\r
+ public boolean getShowSequenceFeatures()\r
+ {\r
+ return showSequenceFeatures;\r
+ }\r
+\r
\r
public void updateConservation()\r
{\r
annotations,\r
0f, // cons.qualityRange[0].floatValue(),\r
11f, // cons.qualityRange[1].floatValue()\r
- AlignmentAnnotation.LINE_GRAPH);\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
- AlignmentAnnotation.LINE_GRAPH);\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, AlignmentAnnotation.LINE_GRAPH);\r
+ "PID", annotations, 0f, 100f, AlignmentAnnotation.BAR_GRAPH);\r
if (showConsensus)\r
{\r
alignment.addAnnotation(consensus);\r