/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.image.*;
-import javax.swing.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
-import jalview.datamodel.*;
+import java.awt.BasicStroke;
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
+import java.awt.Shape;
+import java.awt.image.BufferedImage;
+import java.util.List;
+
+import javax.swing.JComponent;
/**
* DOCUMENT ME!
public SeqCanvas(AlignmentPanel ap)
{
this.av = ap.av;
+ updateViewport();
fr = new FeatureRenderer(ap);
sr = new SequenceRenderer(av);
setLayout(new BorderLayout());
return fr;
}
+ int charHeight = 0, charWidth = 0;
+
+ private void updateViewport()
+ {
+ charHeight = av.getCharHeight();
+ charWidth = av.getCharWidth();
+ }
+
/**
* DOCUMENT ME!
*
* @param ypos
* DOCUMENT ME!
*/
- void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+ private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
{
+ updateViewport();
int scalestartx = startx - (startx % 10) + 10;
g.setColor(Color.black);
-
// NORTH SCALE
for (int i = scalestartx; i < endx; i += 10)
{
value = av.getColumnSelection().adjustForHiddenColumns(value);
}
- g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
- ypos - (av.charHeight / 2));
+ g.drawString(String.valueOf(value), (i - startx - 1) * charWidth,
+ ypos - (charHeight / 2));
- g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
- (ypos + 2) - (av.charHeight / 2),
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
- ypos - 2);
+ g.drawLine(((i - startx - 1) * charWidth) + (charWidth / 2),
+ (ypos + 2) - (charHeight / 2), ((i - startx - 1) * charWidth)
+ + (charWidth / 2), ypos - 2);
}
}
void drawWestScale(Graphics g, int startx, int endx, int ypos)
{
FontMetrics fm = getFontMetrics(av.getFont());
- ypos += av.charHeight;
+ ypos += charHeight;
if (av.hasHiddenColumns())
{
if (value != -1)
{
int x = LABEL_WEST - fm.stringWidth(String.valueOf(value))
- - av.charWidth / 2;
- g.drawString(value + "", x, (ypos + (i * av.charHeight))
- - (av.charHeight / 5));
+ - charWidth / 2;
+ g.drawString(value + "", x, (ypos + (i * charHeight))
+ - (charHeight / 5));
}
}
}
*/
void drawEastScale(Graphics g, int startx, int endx, int ypos)
{
- ypos += av.charHeight;
+ ypos += charHeight;
if (av.hasHiddenColumns())
{
if (value != -1)
{
- g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))
- - (av.charHeight / 5));
+ g.drawString(String.valueOf(value), 0, (ypos + (i * charHeight))
+ - (charHeight / 5));
}
}
}
*/
public void fastPaint(int horizontal, int vertical)
{
- if (fastpainting)
+ if (fastpainting || gg == null)
{
return;
}
fastpainting = true;
- if (gg == null)
- {
- return;
- }
-
fastPaint = true;
-
- gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,
- imgWidth, imgHeight, -horizontal * av.charWidth, -vertical
- * av.charHeight);
+ updateViewport();
+ gg.copyArea(horizontal * charWidth, vertical * charHeight, imgWidth,
+ imgHeight, -horizontal * charWidth, -vertical * charHeight);
int sr = av.startRes;
int er = av.endRes;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
er++;
- transX = (er - sr - horizontal) * av.charWidth;
+ transX = (er - sr - horizontal) * charWidth;
sr = er - horizontal;
}
else if (horizontal < 0)
}
else
{
- transY = imgHeight - (vertical * av.charHeight);
+ transY = imgHeight - (vertical * charHeight);
}
}
else if (vertical < 0)
// Set this to false to force a full panel paint
public void paintComponent(Graphics g)
{
+ updateViewport();
BufferedImage lcimg = img; // take reference since other threads may null
// img and call later.
super.paintComponent(g);
imgWidth = getWidth();
imgHeight = getHeight();
- imgWidth -= (imgWidth % av.charWidth);
- imgHeight -= (imgHeight % av.charHeight);
+ imgWidth -= (imgWidth % charWidth);
+ imgHeight -= (imgHeight % charHeight);
if ((imgWidth < 1) || (imgHeight < 1))
{
LABEL_EAST = 0;
LABEL_WEST = 0;
- if (av.scaleRightWrapped)
+ if (av.getScaleRightWrapped())
{
LABEL_EAST = fm.stringWidth(getMask());
}
- if (av.scaleLeftWrapped)
+ if (av.getScaleLeftWrapped())
{
LABEL_WEST = fm.stringWidth(getMask());
}
- return (cwidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
+ return (cwidth - LABEL_EAST - LABEL_WEST) / charWidth;
}
/**
public void drawWrappedPanel(Graphics g, int canvasWidth,
int canvasHeight, int startRes)
{
+ updateViewport();
AlignmentI al = av.getAlignment();
FontMetrics fm = getFontMetrics(av.getFont());
- if (av.scaleRightWrapped)
+ if (av.getScaleRightWrapped())
{
LABEL_EAST = fm.stringWidth(getMask());
}
- if (av.scaleLeftWrapped)
+ if (av.getScaleLeftWrapped())
{
LABEL_WEST = fm.stringWidth(getMask());
}
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = charHeight;
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += charHeight;
}
- int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
- int cHeight = av.getAlignment().getHeight() * av.charHeight;
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / charWidth;
+ int cHeight = av.getAlignment().getHeight() * charHeight;
av.setWrappedWidth(cWidth);
g.setFont(av.getFont());
g.setColor(Color.black);
- if (av.scaleLeftWrapped)
+ if (av.getScaleLeftWrapped())
{
drawWestScale(g, startRes, endx, ypos);
}
- if (av.scaleRightWrapped)
+ if (av.getScaleRightWrapped())
{
g.translate(canvasWidth - LABEL_EAST, 0);
drawEastScale(g, startRes, endx, ypos);
g.translate(LABEL_WEST, 0);
- if (av.scaleAboveWrapped)
+ if (av.getScaleAboveWrapped())
{
drawNorthScale(g, startRes, endx, ypos);
}
- if (av.hasHiddenColumns() && av.showHiddenMarkers)
+ if (av.hasHiddenColumns() && av.getShowHiddenMarkers())
{
g.setColor(Color.blue);
int res;
continue;
}
- gg.fillPolygon(new int[]
- { res * av.charWidth - av.charHeight / 4,
- res * av.charWidth + av.charHeight / 4, res * av.charWidth },
- new int[]
- { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),
- ypos - (av.charHeight / 2) + 8 }, 3);
+ gg.fillPolygon(
+ new int[] { res * charWidth - charHeight / 4,
+ res * charWidth + charHeight / 4, res * charWidth },
+ new int[] { ypos - (charHeight / 2),
+ ypos - (charHeight / 2), ypos - (charHeight / 2) + 8 },
+ 3);
}
}
if (clip == null)
{
- g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+ g.setClip(0, 0, cWidth * charWidth, canvasHeight);
}
else
{
- g.setClip(0, (int) clip.getBounds().getY(), cWidth * av.charWidth,
+ g.setClip(0, (int) clip.getBounds().getY(), cWidth * charWidth,
(int) clip.getBounds().getHeight());
}
drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
g.translate(0, cHeight + ypos + 3);
if (annotations == null)
annotations = new AnnotationPanel(av);
}
- annotations.renderer.drawComponent(annotations, av, (Graphics2D) g,
- -1, startRes, endx + 1);
+ annotations.renderer.drawComponent(annotations, av, g, -1,
+ startRes, endx + 1);
g.translate(0, -cHeight - ypos - 3);
}
g.setClip(clip);
int getAnnotationHeight()
{
- if (!av.showAnnotation)
+ if (!av.isShowAnnotation())
{
return 0;
}
* @param offset
* DOCUMENT ME!
*/
- void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
- int endSeq, int offset)
+ public void drawPanel(Graphics g1, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
{
+ updateViewport();
if (!av.hasHiddenColumns())
{
draw(g1, startRes, endRes, startSeq, endSeq, offset);
}
else
{
- java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+ List<int[]> regions = av.getColumnSelection().getHiddenColumns();
int screenY = 0;
int blockStart = startRes;
int blockEnd = endRes;
- for (int i = 0; regions != null && i < regions.size(); i++)
+ for (int[] region : regions)
{
- int[] region = (int[]) regions.elementAt(i);
int hideStart = region[0];
int hideEnd = region[1];
blockEnd = hideStart - 1;
- g1.translate(screenY * av.charWidth, 0);
+ g1.translate(screenY * charWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
{
g1.setColor(Color.blue);
- g1.drawLine((blockEnd - blockStart + 1) * av.charWidth - 1,
- 0 + offset, (blockEnd - blockStart + 1) * av.charWidth
- - 1, (endSeq - startSeq) * av.charHeight + offset);
+ g1.drawLine((blockEnd - blockStart + 1) * charWidth - 1,
+ 0 + offset, (blockEnd - blockStart + 1) * charWidth - 1,
+ (endSeq - startSeq) * charHeight + offset);
}
- g1.translate(-screenY * av.charWidth, 0);
+ g1.translate(-screenY * charWidth, 0);
screenY += blockEnd - blockStart + 1;
blockStart = hideEnd + 1;
}
if (screenY <= (endRes - startRes))
{
blockEnd = blockStart + (endRes - startRes) - screenY;
- g1.translate(screenY * av.charWidth, 0);
+ g1.translate(screenY * charWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
- g1.translate(-screenY * av.charWidth, 0);
+ g1.translate(-screenY * charWidth, 0);
}
}
// int startRes, int endRes, int startSeq, int endSeq, int x, int y,
// int x1, int x2, int y1, int y2, int startx, int starty,
- void draw(Graphics g, int startRes, int endRes, int startSeq, int endSeq,
- int offset)
+ private void draw(Graphics g, int startRes, int endRes, int startSeq,
+ int endSeq, int offset)
{
g.setFont(av.getFont());
- sr.prepare(g, av.renderGaps);
+ sr.prepare(g, av.isRenderGaps());
SequenceI nextSeq;
continue;
}
sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
- startRes, endRes, offset + ((i - startSeq) * av.charHeight));
+ startRes, endRes, offset + ((i - startSeq) * charHeight));
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * av.charHeight));
+ + ((i - startSeq) * charHeight));
}
// / Highlight search Results once all sequences have been drawn
{
sr.drawHighlightedText(nextSeq, visibleResults[r],
visibleResults[r + 1], (visibleResults[r] - startRes)
- * av.charWidth, offset
- + ((i - startSeq) * av.charHeight));
+ * charWidth, offset
+ + ((i - startSeq) * charHeight));
}
}
}
if (av.cursorMode && cursorY == i && cursorX >= startRes
&& cursorX <= endRes)
{
- sr.drawCursor(nextSeq, cursorX,
- (cursorX - startRes) * av.charWidth, offset
- + ((i - startSeq) * av.charHeight));
+ sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * charWidth,
+ offset + ((i - startSeq) * charHeight));
}
}
int sy = -1;
int ex = -1;
int groupIndex = -1;
- int visWidth = (endRes - startRes + 1) * av.charWidth;
+ int visWidth = (endRes - startRes + 1) * charWidth;
if ((group == null) && (av.getAlignment().getGroups().size() > 0))
{
- group = (SequenceGroup) av.getAlignment().getGroups().get(0);
+ group = av.getAlignment().getGroups().get(0);
groupIndex = 0;
}
for (i = startSeq; i < endSeq; i++)
{
- sx = (group.getStartRes() - startRes) * av.charWidth;
- sy = offset + ((i - startSeq) * av.charHeight);
- ex = (((group.getEndRes() + 1) - group.getStartRes()) * av.charWidth) - 1;
+ sx = (group.getStartRes() - startRes) * charWidth;
+ sy = offset + ((i - startSeq) * charHeight);
+ ex = (((group.getEndRes() + 1) - group.getStartRes()) * charWidth) - 1;
if (sx + ex < 0 || sx > visWidth)
{
continue;
}
- if ((sx <= (endRes - startRes) * av.charWidth)
+ if ((sx <= (endRes - startRes) * charWidth)
&& group.getSequences(null).contains(
av.getAlignment().getSequenceAt(i)))
{
&& !group.getSequences(null).contains(
av.getAlignment().getSequenceAt(i + 1)))
{
- bottom = sy + av.charHeight;
+ bottom = sy + charHeight;
}
if (!inGroup)
if (group == av.getSelectionGroup())
{
g.setStroke(new BasicStroke(1, BasicStroke.CAP_BUTT,
- BasicStroke.JOIN_ROUND, 3f, new float[]
- { 5f, 3f }, 0f));
+ BasicStroke.JOIN_ROUND, 3f, new float[] { 5f, 3f },
+ 0f));
g.setColor(Color.RED);
}
else
ex = visWidth;
}
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+ else if (sx + ex >= (endRes - startRes + 1) * charWidth)
{
- ex = (endRes - startRes + 1) * av.charWidth;
+ ex = (endRes - startRes + 1) * charWidth;
}
if (top != -1)
if (inGroup)
{
- sy = offset + ((i - startSeq) * av.charHeight);
+ sy = offset + ((i - startSeq) * charHeight);
if (sx >= 0 && sx < visWidth)
{
g.drawLine(sx, oldY, sx, sy);
{
ex = visWidth;
}
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+ else if (sx + ex >= (endRes - startRes + 1) * charWidth)
{
- ex = (endRes - startRes + 1) * av.charWidth;
+ ex = (endRes - startRes + 1) * charWidth;
}
if (top != -1)
break;
}
- group = (SequenceGroup) av.getAlignment().getGroups()
- .get(groupIndex);
+ group = av.getAlignment().getGroups().get(groupIndex);
} while (groupIndex < av.getAlignment().getGroups().size());
git://source.jalview.org / jalview.git / blobdiff