- this.alignment = align;
- }
-
- public void setWrapAlignment(boolean state)
- {
- wrapAlignment = state;
- }
-
- public void setShowText(boolean state)
- {
- showText = state;
- }
-
- public void setRenderGaps(boolean state)
- {
- renderGaps = state;
- }
-
- public boolean getColourText()
- {
- return showColourText;
- }
-
- public void setColourText(boolean state)
- {
- showColourText = state;
- }
-
- public void setShowBoxes(boolean state)
- {
- showBoxes = state;
- }
-
- public boolean getWrapAlignment()
- {
- return wrapAlignment;
- }
-
- public boolean getShowText()
- {
- return showText;
- }
-
- public boolean getShowBoxes()
- {
- return showBoxes;
- }
-
- public char getGapCharacter()
- {
- return getAlignment().getGapCharacter();
- }
-
- public void setGapCharacter(char gap)
- {
- if (getAlignment() != null)
- {
- getAlignment().setGapCharacter(gap);
- }
- }
-
- public void setThreshold(int thresh)
- {
- threshold = thresh;
- }
-
- public int getThreshold()
- {
- return threshold;
- }
-
- public void setIncrement(int inc)
- {
- increment = inc;
- }
-
- public int getIncrement()
- {
- return increment;
- }
-
- public void setHiddenColumns(ColumnSelection colsel)
- {
- this.colSel = colsel;
- if (colSel.getHiddenColumns() != null)
- {
- hasHiddenColumns = true;
- }
- }
-
- public ColumnSelection getColumnSelection()
- {
- return colSel;
- }
-
- public void resetSeqLimits(int height)
- {
- setEndSeq(height / getCharHeight());
- }
-
- public void setCurrentTree(NJTree tree)
- {
- currentTree = tree;
- }
-
- public NJTree getCurrentTree()
- {
- return currentTree;
- }
-
- public void setColourAppliesToAllGroups(boolean b)
- {
- colourAppliesToAllGroups = b;
- }
-
- public boolean getColourAppliesToAllGroups()
- {
- return colourAppliesToAllGroups;
- }
-
- public boolean getShowJVSuffix()
- {
- return showJVSuffix;
- }
-
- public void setShowJVSuffix(boolean b)
- {
- showJVSuffix = b;
- }
-
- public boolean getShowAnnotation()
- {
- return showAnnotation;
- }
-
- public void setShowAnnotation(boolean b)
- {
- showAnnotation = b;
- }
-
- public boolean getScaleAboveWrapped()
- {
- return scaleAboveWrapped;
- }
-
- public boolean getScaleLeftWrapped()
- {
- return scaleLeftWrapped;
- }
-
- public boolean getScaleRightWrapped()
- {
- return scaleRightWrapped;
- }
-
- public void setScaleAboveWrapped(boolean b)
- {
- scaleAboveWrapped = b;
- }
-
- public void setScaleLeftWrapped(boolean b)
- {
- scaleLeftWrapped = b;
- }
-
- public void setScaleRightWrapped(boolean b)
- {
- scaleRightWrapped = b;
- }
-
- public void setIgnoreGapsConsensus(boolean b)
- {
- ignoreGapsInConsensusCalculation = b;
- updateConsensus(null);
- if (globalColourScheme != null)
- {
- globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
- ignoreGapsInConsensusCalculation);
-
- }