- conservationColourSelected = b;
- }
-
- public boolean getAbovePIDThreshold()
- {
- return abovePIDThreshold;
- }
-
- public void setAbovePIDThreshold(boolean b)
- {
- abovePIDThreshold = b;
- }
-
- public int getStartRes()
- {
- return startRes;
- }
-
- public int getEndRes()
- {
- return endRes;
- }
-
- public int getStartSeq()
- {
- return startSeq;
- }
-
- public void setGlobalColourScheme(ColourSchemeI cs)
- {
- globalColourScheme = cs;
- }
-
- public ColourSchemeI getGlobalColourScheme()
- {
- return globalColourScheme;
- }
-
- public void setStartRes(int res)
- {
- this.startRes = res;
- }
-
- public void setStartSeq(int seq)
- {
- this.startSeq = seq;
- }
-
- public void setEndRes(int res)
- {
- if (res > alignment.getWidth() - 1)
- {
- // log.System.out.println(" Corrected res from " + res + " to maximum " +
- // (alignment.getWidth()-1));
- res = alignment.getWidth() - 1;
- }
- if (res < 0)
- {
- res = 0;
- }
- this.endRes = res;
- }
-
- public void setEndSeq(int seq)
- {
- if (seq > alignment.getHeight())
- {
- seq = alignment.getHeight();
- }
- if (seq < 0)
- {
- seq = 0;
- }
- this.endSeq = seq;
- }
-
- public int getEndSeq()
- {
- return endSeq;
- }
-
- java.awt.Frame nullFrame;
-
- protected FeatureSettings featureSettings = null;
-
- public void setFont(Font f)
- {
- font = f;
- if (nullFrame == null)
- {
- nullFrame = new java.awt.Frame();
- nullFrame.addNotify();
- }
-
- java.awt.FontMetrics fm = nullFrame.getGraphics().getFontMetrics(font);
- setCharHeight(fm.getHeight());
- charWidth = fm.charWidth('M');
-
- if (upperCasebold)
- {
- Font f2 = new Font(f.getName(), Font.BOLD, f.getSize());
- fm = nullFrame.getGraphics().getFontMetrics(f2);
- charWidth = fm.stringWidth("MMMMMMMMMMM") / 10;
- }
- }
-
- public Font getFont()
- {
- return font;
- }
-
- public int getCharWidth()
- {
- return charWidth;
- }
-
- public void setCharHeight(int h)
- {
- this.charHeight = h;
- }
-
- public int getCharHeight()
- {
- return charHeight;
- }
-
- public void setWrappedWidth(int w)
- {
- this.wrappedWidth = w;
- }
-
- public int getwrappedWidth()
- {
- return wrappedWidth;
- }
-
- public AlignmentI getAlignment()
- {
- return alignment;
- }
-
- public void setAlignment(AlignmentI align)
- {
- 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;