/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.ResidueProperties;
import jalview.schemes.UserColourScheme;
+import jalview.util.Comparison;
+import jalview.util.Format;
import java.io.BufferedReader;
import java.io.FileReader;
}
/**
- * convenience method for pre-2.9 annotation files which have no view, hidden
- * columns or hidden row keywords.
+ * convenience method for pre-2.8.3 annotation files which have no view,
+ * hidden columns or hidden row keywords.
*
* @param annotations
* @param list
graphLine.append("\t");
graphLine.append(row.getThreshold().label);
graphLine.append("\t");
- graphLine.append(jalview.util.Format.getHexString(row
- .getThreshold().colour));
+ graphLine
+ .append(Format.getHexString(row.getThreshold().colour));
graphLine.append(newline);
}
&& j < row.annotations.length; j++)
{
if (refSeq != null
- && jalview.util.Comparison.isGap(refSeq.getCharAt(j)))
+ && Comparison.isGap(refSeq.getCharAt(j)))
{
continue;
}
{
text.append(comma
+ "["
- + jalview.util.Format
+ + Format
.getHexString(row.annotations[j].colour)
+ "]");
comma = ",";
colours.append("COLOUR\t");
colours.append(row.label);
colours.append("\t");
- colours.append(jalview.util.Format.getHexString(color));
+ colours.append(Format.getHexString(color));
colours.append(newline);
}
if (row.scaleColLabel || row.showAllColLabels
}
}
text.append("outlineColour=");
- text.append(jalview.util.Format.getHexString(sg.getOutlineColour()));
+ text.append(Format.getHexString(sg.getOutlineColour()));
text.append("\t");
text.append("displayBoxes=");
if (sg.textColour != java.awt.Color.black)
{
text.append("textCol1=");
- text.append(jalview.util.Format.getHexString(sg.textColour));
+ text.append(Format.getHexString(sg.textColour));
text.append("\t");
}
if (sg.textColour2 != java.awt.Color.white)
{
text.append("textCol2=");
- text.append(jalview.util.Format.getHexString(sg.textColour2));
+ text.append(Format.getHexString(sg.textColour2));
text.append("\t");
}
if (sg.thresholdTextColour != 0)
if (sg.idColour != null)
{
text.append("idColour=");
- text.append(jalview.util.Format.getHexString(sg.idColour));
+ text.append(Format.getHexString(sg.idColour));
text.append("\t");
}
if (sg.isHidereps())