import jalview.schemes.ResidueProperties;
import jalview.schemes.ZappoColourScheme;
import jalview.util.Platform;
+import jalview.viewmodel.AlignmentViewport.AutoAnnotation;
import java.awt.BasicStroke;
import java.awt.Color;
boolean validRes, boolean validEnd)
{
g.setColor(STEM_COLOUR);
- int sCol = (lastSSX / charWidth) + startRes;
+ int sCol = (lastSSX / charWidth)
+ + hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
// System.out.println(nonCanColor);
g.setColor(nonCanColor);
- int sCol = (lastSSX / charWidth) + startRes;
+ int sCol = (lastSSX / charWidth)
+ + hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
// properties/rendering attributes as a global 'alignment group' which holds
// all vis settings for the alignment as a whole rather than a subset
//
- if (aa.autoCalculated && (aa.label.startsWith("Consensus")
- || aa.label.startsWith("cDNA Consensus")))
+ if (aa.autoCalculated
+ && (aa.label.startsWith(AutoAnnotation.CONSENSUS.label)
+ || aa.label.startsWith(
+ AutoAnnotation.CDNA_CONSENSUS.label)))
{
- boolean forComplement = aa.label.startsWith("cDNA Consensus");
+ boolean forComplement = aa.label
+ .startsWith(AutoAnnotation.CDNA_CONSENSUS.label);
if (aa.groupRef != null && aa.groupRef.consensusData != null
&& aa.groupRef.isShowSequenceLogo())
{
}
else
{
- if (aa.autoCalculated && aa.label.startsWith("StrucConsensus"))
+ if (aa.autoCalculated && aa.label
+ .startsWith(AutoAnnotation.STRUCTURE_CONSENSUS.label))
{
// TODO implement group structure consensus
/*
{
if (hasHiddenColumns)
{
- column = hiddenColumns.adjustForHiddenColumns(startRes + x);
+ column = hiddenColumns.visibleToAbsoluteColumn(startRes + x);
if (column > row_annotations.length - 1)
{
break;
{
g.setColor(HELIX_COLOUR);
- int sCol = (lastSSX / charWidth) + startRes;
+ int sCol = (lastSSX / charWidth)
+ + hiddenColumns.visibleToAbsoluteColumn(startRes);
int x1 = lastSSX;
int x2 = (x * charWidth);
column = sRes + x;
if (hasHiddenColumns)
{
- column = hiddenColumns.adjustForHiddenColumns(column);
+ column = hiddenColumns.visibleToAbsoluteColumn(column);
}
if (column > aaMax)
column = sRes + x;
if (hasHiddenColumns)
{
- column = hiddenColumns.adjustForHiddenColumns(column);
+ column = hiddenColumns.visibleToAbsoluteColumn(column);
}
if (column > aaMax)