- int startRes;
- int endRes;
- int startSeq;
- int endSeq;
- boolean showJVSuffix = true;
- boolean showText = true;
- boolean showColourText = false;
- boolean showBoxes = true;
- boolean wrapAlignment = false;
- boolean renderGaps = true;
- boolean showSequenceFeatures = false;
- boolean showAnnotation = true;
- boolean colourAppliesToAllGroups = true;
- ColourSchemeI globalColourScheme = null;
- boolean conservationColourSelected = false;
- boolean abovePIDThreshold = false;
- SequenceGroup selectionGroup;
- int charHeight;
- int charWidth;
- boolean validCharWidth;
- int wrappedWidth;
- Font font;
- boolean seqNameItalics;
- AlignmentI alignment;
- ColumnSelection colSel = new ColumnSelection();
- int threshold;
- int increment;
- NJTree currentTree = null;
- boolean scaleAboveWrapped = false;
- boolean scaleLeftWrapped = true;
- boolean scaleRightWrapped = true;
- boolean hasHiddenColumns = false;
- boolean hasHiddenRows = false;
- boolean showHiddenMarkers = true;
-
- boolean cursorMode = false;
-
- // The following vector holds the features which are
- // currently visible, in the correct order or rendering
- Hashtable featuresDisplayed = null;
-
- /** DOCUMENT ME!! */
- public Hashtable[] hconsensus;
- AlignmentAnnotation consensus;
- AlignmentAnnotation conservation;
- AlignmentAnnotation quality;
- boolean autoCalculateConsensus = true;
-
- /** DOCUMENT ME!! */
- public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
-
- // JBPNote Prolly only need this in the applet version.
+ int startRes;
+ int endRes;
+ int startSeq;
+ int endSeq;
+ boolean showJVSuffix = true;
+ boolean showText = true;
+ boolean showColourText = false;
+ boolean showBoxes = true;
+ boolean wrapAlignment = false;
+ boolean renderGaps = true;
+ boolean showSequenceFeatures = false;
+ boolean showAnnotation = true;
+ boolean colourAppliesToAllGroups = true;
+ ColourSchemeI globalColourScheme = null;
+ boolean conservationColourSelected = false;
+ boolean abovePIDThreshold = false;
+ SequenceGroup selectionGroup;
+ int charHeight;
+ int charWidth;
+ boolean validCharWidth;
+ int wrappedWidth;
+ Font font;
+ boolean seqNameItalics;
+ AlignmentI alignment;
+ ColumnSelection colSel = new ColumnSelection();
+ int threshold;
+ int increment;
+ NJTree currentTree = null;
+ boolean scaleAboveWrapped = false;
+ boolean scaleLeftWrapped = true;
+ boolean scaleRightWrapped = true;
+ boolean hasHiddenColumns = false;
+ boolean hasHiddenRows = false;
+ boolean showHiddenMarkers = true;
+
+ boolean cursorMode = false;
+
+ // The following vector holds the features which are
+ // currently visible, in the correct order or rendering
+ Hashtable featuresDisplayed = null;
+
+
+ /** DOCUMENT ME!! */
+ public Hashtable [] hconsensus;
+ AlignmentAnnotation consensus;
+ AlignmentAnnotation conservation;
+ AlignmentAnnotation quality;
+ boolean autoCalculateConsensus = true;
+
+ /** DOCUMENT ME!! */
+ public int ConsPercGaps = 25; // JBPNote : This should be a scalable property!
+
+ // JBPNote Prolly only need this in the applet version.