--- /dev/null
+/*
+ * 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 jalview.api.AlignmentColsCollectionI;
+import jalview.api.AlignmentRowsCollectionI;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.Annotation;
+import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.renderer.seqfeatures.FeatureRenderer;
+import jalview.viewmodel.OverviewDimensions;
+
+import java.awt.Color;
+import java.awt.Graphics;
+import java.awt.image.BufferedImage;
+
+public class OverviewRenderer
+{
+ private FeatureColourFinder finder;
+
+ private jalview.api.SequenceRenderer sr;
+
+ // image to render on
+ private BufferedImage miniMe;
+
+ // raw number of pixels to allocate to each column
+ private float pixelsPerCol;
+
+ // raw number of pixels to allocate to each row
+ private float pixelsPerSeq;
+
+ public OverviewRenderer(jalview.api.SequenceRenderer seqRenderer,
+ FeatureRenderer fr, OverviewDimensions od)
+ // FeatureColourFinder colfinder, OverviewDimensions od)
+ {
+ sr = seqRenderer;
+ finder = new FeatureColourFinder(fr); // colfinder;
+
+ pixelsPerCol = od.getPixelsPerCol();
+ pixelsPerSeq = od.getPixelsPerSeq();
+ miniMe = new BufferedImage(od.getWidth(), od.getHeight(),
+ BufferedImage.TYPE_INT_RGB);
+ }
+
+ /**
+ * Draw alignment rows and columns onto an image
+ *
+ * @param rit
+ * Iterator over rows to be drawn
+ * @param cit
+ * Iterator over columns to be drawn
+ * @return image containing the drawing
+ */
+ public BufferedImage draw(AlignmentRowsCollectionI rows,
+ AlignmentColsCollectionI cols)
+ {
+ int rgbcolor = Color.white.getRGB();
+ int seqIndex = 0;
+ int pixelRow = 0;
+ for (int alignmentRow : rows)
+ {
+ // get details of this alignment row
+ boolean hidden = rows.isHidden(alignmentRow);
+ SequenceI seq = rows.getSequence(alignmentRow);
+
+ // calculate where this row extends to in pixels
+ int endRow = Math.min(Math.round((seqIndex + 1) * pixelsPerSeq) - 1,
+ miniMe.getHeight() - 1);
+
+ int colIndex = 0;
+ int pixelCol = 0;
+ for (int alignmentCol : cols)
+ {
+ // calculate where this column extends to in pixels
+ int endCol = Math.min(
+ Math.round((colIndex + 1) * pixelsPerCol) - 1,
+ miniMe.getWidth() - 1);
+
+ // don't do expensive colour determination if we're not going to use it
+ // NB this is important to avoid performance issues in the overview
+ // panel
+ if (pixelCol <= endCol)
+ {
+ // determine the colour based on the sequence and column position
+ rgbcolor = getColumnColourFromSequence(seq,
+ hidden || cols.isHidden(alignmentCol), alignmentCol,
+ finder);
+
+ // fill in the appropriate number of pixels
+ for (int row = pixelRow; row <= endRow; ++row)
+ {
+ for (int col = pixelCol; col <= endCol; ++col)
+ {
+ miniMe.setRGB(col, row, rgbcolor);
+ }
+ }
+
+ pixelCol = endCol + 1;
+ }
+ colIndex++;
+ }
+ pixelRow = endRow + 1;
+ seqIndex++;
+ }
+ return miniMe;
+ }
+
+ /*
+ * Find the colour of a sequence at a specified column position
+ */
+ private int getColumnColourFromSequence(jalview.datamodel.SequenceI seq,
+ boolean isHidden, int lastcol, FeatureColourFinder fcfinder)
+ {
+ Color color = Color.white;
+
+ if ((seq != null) && (seq.getLength() > lastcol))
+ {
+ color = sr.getResidueColour(seq, lastcol, fcfinder);
+ }
+
+ if (isHidden)
+ {
+ color = color.darker().darker();
+ }
+
+ return color.getRGB();
+ }
+
+ /**
+ * Draw the alignment annotation in the overview panel
+ *
+ * @param g
+ * the graphics object to draw on
+ * @param anno
+ * alignment annotation information
+ * @param charWidth
+ * alignment character width value
+ * @param y
+ * y-position for the annotation graph
+ * @param cols
+ * the collection of columns used in the overview panel
+ */
+ public void drawGraph(Graphics g, AlignmentAnnotation anno, int charWidth,
+ int y, AlignmentColsCollectionI cols)
+ {
+ Annotation[] annotations = anno.annotations;
+ g.setColor(Color.white);
+ g.fillRect(0, 0, miniMe.getWidth(), y);
+
+ int height;
+ int colIndex = 0;
+ int pixelCol = 0;
+ for (int alignmentCol : cols)
+ {
+ if (alignmentCol >= annotations.length)
+ {
+ break; // no more annotations to draw here
+ }
+ else
+ {
+ int endCol = Math.min(
+ Math.round((colIndex + 1) * pixelsPerCol) - 1,
+ miniMe.getWidth() - 1);
+
+ if (annotations[alignmentCol] != null)
+ {
+ if (annotations[alignmentCol].colour == null)
+ {
+ g.setColor(Color.black);
+ }
+ else
+ {
+ g.setColor(annotations[alignmentCol].colour);
+ }
+
+ height = (int) ((annotations[alignmentCol].value / anno.graphMax) * y);
+ if (height > y)
+ {
+ height = y;
+ }
+
+ g.fillRect(pixelCol, y - height, endCol - pixelCol + 1, height);
+ }
+ pixelCol = endCol + 1;
+ colIndex++;
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff