+ SequenceI sq = new Sequence("Consensus", seqs.toString());
+ sq.setDescription("Percentage Identity Consensus " +
+ ( (ignoreGapsInConsensusCalculation) ? " without gaps" :
+ ""));
+ return sq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public SequenceGroup getSelectionGroup()
+ {
+ return selectionGroup;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param sg DOCUMENT ME!
+ */
+ public void setSelectionGroup(SequenceGroup sg)
+ {
+ selectionGroup = sg;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getConservationSelected()
+ {
+ return conservationColourSelected;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setConservationSelected(boolean b)
+ {
+ conservationColourSelected = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getAbovePIDThreshold()
+ {
+ return abovePIDThreshold;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setAbovePIDThreshold(boolean b)
+ {
+ abovePIDThreshold = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getStartRes()
+ {
+ return startRes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEndRes()
+ {
+ return endRes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getStartSeq()
+ {
+ return startSeq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param cs DOCUMENT ME!
+ */
+ public void setGlobalColourScheme(ColourSchemeI cs)
+ {
+ globalColourScheme = cs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ColourSchemeI getGlobalColourScheme()
+ {
+ return globalColourScheme;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param res DOCUMENT ME!
+ */
+ public void setStartRes(int res)
+ {
+ this.startRes = res;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq DOCUMENT ME!
+ */
+ public void setStartSeq(int seq)
+ {
+ this.startSeq = seq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param res DOCUMENT ME!
+ */
+ 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;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param seq DOCUMENT ME!
+ */
+ public void setEndSeq(int seq)
+ {
+ if (seq > alignment.getHeight())
+ {
+ seq = alignment.getHeight();
+ }
+
+ if (seq < 0)
+ {
+ seq = 0;
+ }
+
+ this.endSeq = seq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getEndSeq()
+ {
+ return endSeq;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param f DOCUMENT ME!
+ */
+ public void setFont(Font f)
+ {
+ font = f;
+
+ Container c = new Container();
+
+ java.awt.FontMetrics fm = c.getFontMetrics(font);
+ setCharHeight(fm.getHeight());
+ setCharWidth(fm.charWidth('M'));
+ validCharWidth = true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public Font getFont()
+ {
+ return font;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param w DOCUMENT ME!
+ */
+ public void setCharWidth(int w)
+ {
+ this.charWidth = w;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getCharWidth()
+ {
+ return charWidth;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param h DOCUMENT ME!
+ */
+ public void setCharHeight(int h)
+ {
+ this.charHeight = h;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getCharHeight()
+ {
+ return charHeight;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param w DOCUMENT ME!
+ */
+ public void setWrappedWidth(int w)
+ {
+ this.wrappedWidth = w;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getWrappedWidth()
+ {
+ return wrappedWidth;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public AlignmentI getAlignment()
+ {
+ return alignment;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param align DOCUMENT ME!
+ */
+ public void setAlignment(AlignmentI align)
+ {
+ this.alignment = align;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state DOCUMENT ME!
+ */
+ public void setWrapAlignment(boolean state)
+ {
+ wrapAlignment = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state DOCUMENT ME!
+ */
+ public void setShowText(boolean state)
+ {
+ showText = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state DOCUMENT ME!
+ */
+ public void setRenderGaps(boolean state)
+ {
+ renderGaps = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getColourText()
+ {
+ return showColourText;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state DOCUMENT ME!
+ */
+ public void setColourText(boolean state)
+ {
+ showColourText = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param state DOCUMENT ME!
+ */
+ public void setShowBoxes(boolean state)
+ {
+ showBoxes = state;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getWrapAlignment()
+ {
+ return wrapAlignment;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowText()
+ {
+ return showText;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowBoxes()
+ {
+ return showBoxes;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public char getGapCharacter()
+ {
+ return getAlignment().getGapCharacter();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param gap DOCUMENT ME!
+ */
+ public void setGapCharacter(char gap)
+ {
+ if (getAlignment() != null)
+ {
+ getAlignment().setGapCharacter(gap);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param thresh DOCUMENT ME!
+ */
+ public void setThreshold(int thresh)
+ {
+ threshold = thresh;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param inc DOCUMENT ME!
+ */
+ public void setIncrement(int inc)
+ {
+ increment = inc;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getIncrement()
+ {
+ return increment;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public ColumnSelection getColumnSelection()
+ {
+ return colSel;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param tree DOCUMENT ME!
+ */
+ public void setCurrentTree(NJTree tree)
+ {
+ currentTree = tree;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public NJTree getCurrentTree()
+ {
+ return currentTree;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setColourAppliesToAllGroups(boolean b)
+ {
+ colourAppliesToAllGroups = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getColourAppliesToAllGroups()
+ {
+ return colourAppliesToAllGroups;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowJVSuffix()
+ {
+ return showJVSuffix;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setShowJVSuffix(boolean b)
+ {
+ showJVSuffix = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getShowAnnotation()
+ {
+ return showAnnotation;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setShowAnnotation(boolean b)
+ {
+ showAnnotation = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getScaleAboveWrapped()
+ {
+ return scaleAboveWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getScaleLeftWrapped()
+ {
+ return scaleLeftWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public boolean getScaleRightWrapped()
+ {
+ return scaleRightWrapped;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setScaleAboveWrapped(boolean b)
+ {
+ scaleAboveWrapped = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setScaleLeftWrapped(boolean b)
+ {
+ scaleLeftWrapped = b;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b DOCUMENT ME!
+ */
+ public void setScaleRightWrapped(boolean b)
+ {
+ scaleRightWrapped = b;
+ }
+
+ /**
+ * Property change listener for changes in alignment
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public void addPropertyChangeListener(
+ java.beans.PropertyChangeListener listener)
+ {
+ changeSupport.addPropertyChangeListener(listener);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param listener DOCUMENT ME!
+ */
+ public void removePropertyChangeListener(
+ java.beans.PropertyChangeListener listener)
+ {
+ changeSupport.removePropertyChangeListener(listener);
+ }
+
+ /**
+ * Property change listener for changes in alignment
+ *
+ * @param prop DOCUMENT ME!
+ * @param oldvalue DOCUMENT ME!
+ * @param newvalue DOCUMENT ME!
+ */
+ public void firePropertyChange(String prop, Object oldvalue, Object newvalue)
+ {
+ changeSupport.firePropertyChange(prop, oldvalue, newvalue);
+ }
+
+ public void setIgnoreGapsConsensus(boolean b, AlignmentPanel ap)
+ {
+ ignoreGapsInConsensusCalculation = b;
+ updateConsensus(ap);
+ if (globalColourScheme != null)
+ {
+ globalColourScheme.setThreshold(globalColourScheme.getThreshold(),
+ ignoreGapsInConsensusCalculation);
+ }
+ }
+
+ public boolean getIgnoreGapsConsensus()
+ {
+ return ignoreGapsInConsensusCalculation;
+ }
+
+ public void setDataset(boolean b)
+ {
+ isDataset = b;
+ }
+
+ public boolean isDataset()
+ {
+ return isDataset;
+ }
+
+ public void hideSelectedColumns()
+ {
+ if (colSel.size() < 1)
+ {
+ return;
+ }
+
+ colSel.hideSelectedColumns();
+ setSelectionGroup(null);
+
+ hasHiddenColumns = true;
+ }
+
+ public void hideColumns(int start, int end)
+ {
+ if (start == end)
+ {
+ colSel.hideColumns(start);
+ }
+ else
+ {
+ colSel.hideColumns(start, end);
+ }
+
+ hasHiddenColumns = true;
+ }