import jalview.io.*;\r
import jalview.analysis.NJTree;\r
import jalview.datamodel.*;\r
+import jalview.schemes.*;\r
import java.util.*;\r
\r
public class AlignViewport\r
boolean showColourText=false;\r
boolean showBoxes=true;\r
boolean wrapAlignment=false;\r
- boolean renderGaps = false;\r
+ boolean renderGaps = true;\r
\r
- boolean groupEdit = false;\r
+ ColourSchemeI globalColourScheme = null;\r
+ boolean conservationColourSelected = false;\r
\r
- RendererI renderer = new SequenceRenderer();\r
+ SequenceGroup rubberbandGroup = null;\r
+\r
+ RendererI renderer = new SequenceRenderer(this);\r
\r
int charHeight;\r
- double charWidth;\r
+ int charWidth;\r
int chunkWidth;\r
int chunkHeight;\r
\r
- Color backgroundColour;\r
-\r
Font font = new Font("SansSerif",Font.PLAIN,10);\r
AlignmentI alignment;\r
\r
- Selection sel = new Selection();\r
+ Selection sel = new Selection(this);\r
ColumnSelection colSel = new ColumnSelection();\r
\r
OutputGenerator og;\r
setFont( font );\r
}\r
\r
- public AlignViewport(int startRes, int endRes,\r
- int startSeq, int endSeq,\r
- boolean showScores,\r
- boolean showText,\r
- boolean showBoxes,\r
- boolean wrapAlignment,\r
- Color backgroundColour) {\r
- this(startRes,endRes,startSeq,endSeq,showScores,showText,showBoxes,wrapAlignment);\r
-\r
- this.backgroundColour = backgroundColour;\r
- }\r
-\r
\r
public String getVisibleConsensus()\r
{\r
return consensus;\r
}\r
\r
+ public SequenceGroup getRubberbandGroup()\r
+ {\r
+ return rubberbandGroup;\r
+ }\r
+\r
+ public void setRubberbandGroup(SequenceGroup sg)\r
+ {\r
+ rubberbandGroup = sg;\r
+ }\r
+\r
+ public boolean getConservationSelected()\r
+ {\r
+ return conservationColourSelected;\r
+ }\r
+\r
+ public void setConservationSelected(boolean b)\r
+ {\r
+ conservationColourSelected = b;\r
+ }\r
\r
public int getStartRes() {\r
return startRes;\r
return startSeq;\r
}\r
\r
+ public void setGlobalColourScheme(ColourSchemeI cs)\r
+ {\r
+ globalColourScheme = cs;\r
+ }\r
+\r
+ public ColourSchemeI getGlobalColourScheme()\r
+ {\r
+ return globalColourScheme;\r
+ }\r
+\r
\r
public void setStartRes(int res) {\r
this.startRes = res;\r
public Font getFont() {\r
return font;\r
}\r
- public void setCharWidth(double w) {\r
+ public void setCharWidth(int w) {\r
this.charWidth = w;\r
}\r
- public double getCharWidth() {\r
+ public int getCharWidth() {\r
return charWidth;\r
}\r
public void setCharHeight(int h) {\r
public boolean getShowBoxes() {\r
return showBoxes;\r
}\r
- // public CommandParser getCommandLog() {\r
- /// return log;\r
- // }\r
- public boolean getGroupEdit() {\r
- return groupEdit;\r
- }\r
- public void setGroupEdit(boolean state) {\r
- groupEdit = state;\r
- }\r
+\r
public char getGapCharacter() {\r
return getAlignment().getGapCharacter();\r
}\r