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
int wrappedWidth;\r
\r
Font font = new Font("SansSerif", Font.PLAIN, 10);\r
+ boolean validCharWidth = true;\r
AlignmentI alignment;\r
\r
ColumnSelection colSel = new ColumnSelection();\r
\r
// The following vector holds the features which are\r
// currently visible, in the correct order or rendering\r
- Hashtable featuresDisplayed = null;\r
+ Hashtable featuresDisplayed;\r
\r
\r
public Vector vconsensus;\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
updateConservation();\r
updateConsensus();\r
\r
- if (applet != null && applet.getParameter("defaultColour") != null)\r
+\r
+ if (applet != null)\r
{\r
- globalColourScheme = ColourSchemeProperty.getColour(alignment,\r
- applet.getParameter("defaultColour"));\r
- if (globalColourScheme != null)\r
+ String colour = applet.getParameter("defaultColour");\r
+\r
+ if(colour == null)\r
+ {\r
+ colour = applet.getParameter("userDefinedColour");\r
+ if(colour !=null)\r
+ colour = "User Defined";\r
+ }\r
+\r
+ if(colour != null)\r
+ {\r
+ globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);\r
+ if (globalColourScheme != null)\r
+ {\r
+ globalColourScheme.setConsensus(vconsensus);\r
+ }\r
+ }\r
+\r
+ if(applet.getParameter("userDefinedColour")!=null)\r
{\r
- globalColourScheme.setConsensus(vconsensus);\r
+ ((UserColourScheme)globalColourScheme).parseAppletParameter(\r
+ applet.getParameter("userDefinedColour"));\r
}\r
+\r
+\r
}\r
}\r
\r
return endSeq;\r
}\r
\r
+ java.awt.Frame nullFrame;\r
public void setFont(Font f)\r
{\r
font = f;\r
- java.awt.Frame temp = new java.awt.Frame();\r
- temp.addNotify();\r
- java.awt.FontMetrics fm = temp.getGraphics().getFontMetrics(font);\r
+ if(nullFrame == null)\r
+ {\r
+ nullFrame = new java.awt.Frame();\r
+ nullFrame.addNotify();\r
+ }\r
+\r
+ java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);\r
setCharHeight(fm.getHeight());\r
setCharWidth(fm.charWidth('M'));\r
}\r