-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
*
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.renderer;
import java.awt.Color;
import java.awt.Graphics;
-import java.util.Iterator;
import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
* shown when no data available from map
*/
Color no_data;
+
/**
* shown for region not currently visible - should normally not see this
*/
Color hidden;
+
/**
* linear shading scheme min/max
*/
/**
*
- * @param no_data - colour when no data available
- * @param hidden - colour if this row is hidden
- * @param maxColor - colour for maximum value of contact
- * @param minColor - colour for minimum value of contact
- * @param selMinColor - min colour if the contact has been selected
- * @param selMaxColor - max colour if contact is selected
+ * @param no_data
+ * - colour when no data available
+ * @param hidden
+ * - colour if this row is hidden
+ * @param maxColor
+ * - colour for maximum value of contact
+ * @param minColor
+ * - colour for minimum value of contact
+ * @param selMinColor
+ * - min colour if the contact has been selected
+ * @param selMaxColor
+ * - max colour if contact is selected
*/
public Shading(Color no_data, Color hidden, Color maxColor,
Color minColor, Color selMinColor, Color selMaxColor)
return new Shading(Color.pink, Color.red,
new Color(247, 252, 245), new Color(0, 68, 28),
- new Color(28, 0, 68), new Color(245,247,252));
+ new Color(28, 0, 68), new Color(245, 247, 252));
}
};
}
HiddenColumns hiddenColumns, ColumnSelection columnSelection,
AlignmentAnnotation _aa, Annotation[] aa_annotations, int sRes,
int eRes, float min, float max, int y)
- {
+ {
if (sRes > aa_annotations.length)
{
return;
// uncomment below to render whole area of matrix as pink
// g.setColor(shade.no_data);
- // g.fillRect(x, topY-_aa.height, (eRes - sRes) * charWidth, _aa.graphHeight);
-
+ // g.fillRect(x, topY-_aa.height, (eRes - sRes) * charWidth,
+ // _aa.graphHeight);
+
boolean showGroups = _aa.isShowGroupsForContactMatrix();
int column;
int aaMax = aa_annotations.length - 1;
ContactMatrixI cm = viewport.getContactMatrix(_aa);
- if (cm==null)
+ if (cm == null)
{
return;
}
if (showGroups && gpcol != null && gpcol != Color.white)
{
// todo - could overlay group as a transparent rectangle ?
- col = new Color(
- (int) (((float) (col.getRed() + gpcol.getRed())) / 2f),
- (int) (((float) (col.getGreen() + gpcol.getGreen()))
- / 2f),
- (int) (((float) (col.getBlue() + gpcol.getBlue())) / 2f));
+ col = new Color((int) ((col.getRed() + gpcol.getRed()) / 2f),
+ (int) ((col.getGreen() + gpcol.getGreen()) / 2f),
+ (int) ((col.getBlue() + gpcol.getBlue()) / 2f));
}
g.setColor(col);
if (cgeom.pixels_step > 1)
{
- g.fillRect(x * charWidth, botY+ht, charWidth, cgeom.pixels_step);
+ g.fillRect(x * charWidth, botY + ht, charWidth,
+ cgeom.pixels_step);
}
else
{
- g.drawLine(x * charWidth, botY+ht, (x + 1) * charWidth, botY+ht);
+ g.drawLine(x * charWidth, botY + ht, (x + 1) * charWidth,
+ botY + ht);
}
}
x++;