int charHeight;\r
int charWidth;\r
int wrappedWidth;\r
- Font font = new Font("SansSerif", Font.PLAIN, 10);\r
+ Font font;\r
AlignmentI alignment;\r
ColumnSelection colSel = new ColumnSelection();\r
int threshold;\r
boolean scaleLeftWrapped = true;\r
boolean scaleRightWrapped = true;\r
boolean hasHiddenColumns = false;\r
+ boolean hasHiddenRows = false;\r
+\r
+ boolean cursorMode = false;\r
\r
// The following vector holds the features which are\r
// currently visible, in the correct order or rendering\r
AlignmentAnnotation consensus;\r
AlignmentAnnotation conservation;\r
AlignmentAnnotation quality;\r
+ boolean autoCalculateConsensus = true;\r
\r
/** DOCUMENT ME!! */\r
public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!\r
\r
boolean antiAlias = false;\r
\r
+ boolean padGaps = false;\r
+\r
\r
public AlignViewport(AlignmentI al, boolean dataset)\r
{\r
showQuality = Cache.getDefault("SHOW_QUALITY", true);\r
showIdentity = Cache.getDefault("SHOW_IDENTITY", true);\r
\r
+ autoCalculateConsensus = Cache.getDefault("AUTO_CALC_CONSENSUS", true);\r
+\r
+ padGaps = Cache.getDefault("PAD_GAPS", false);\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
globalColourScheme.setThreshold(globalColourScheme.getThreshold(), ignoreGapsInConsensusCalculation);\r
}\r
-\r
}\r
\r
public boolean getIgnoreGapsConsensus()\r
{\r
return isDataset;\r
}\r
+\r
+ public void hideSequence(SequenceI seq)\r
+ {\r
+ alignment.getHiddenSequences().hideSequence(seq);\r
+ hasHiddenRows = true;\r
+ }\r
+\r
+ public void showSequence(int index)\r
+ {\r
+ alignment.getHiddenSequences().showSequence(index);\r
+\r
+ if(alignment.getHiddenSequences().getSize()<1)\r
+ hasHiddenRows = false;\r
+ }\r
+\r
+ public int adjustForHiddenSeqs(int alignmentIndex)\r
+ {\r
+ return alignment.getHiddenSequences().adjustForHiddenSeqs(alignmentIndex);\r
+ }\r
}\r