/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.appletgui;
-import java.awt.*;
+import jalview.datamodel.SequenceI;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.beans.PropertyChangeEvent;
+import java.util.List;
-public class IdCanvas
- extends Panel
+public class IdCanvas extends Panel implements ViewportListenerI
{
protected AlignViewport av;
protected boolean showScores = true;
protected int maxIdLength = -1;
+
protected String maxIdStr = null;
+
Image image;
+
Graphics gg;
+
int imgHeight = 0;
+
boolean fastPaint = false;
- java.util.Vector searchResults;
+ List<SequenceI> searchResults;
public IdCanvas(AlignViewport av)
{
setLayout(null);
this.av = av;
PaintRefresher.Register(this, av.getSequenceSetId());
+ av.getRanges().addPropertyChangeListener(this);
}
- public void drawIdString(Graphics gg, SequenceI s, int i, int starty,
- int ypos)
+ public void drawIdString(Graphics gg, boolean hiddenRows, SequenceI s,
+ int i, int starty, int ypos)
{
int charHeight = av.getCharHeight();
if (searchResults != null && searchResults.contains(s))
{
gg.setColor(Color.black);
- gg.fillRect(0, ( (i - starty) * charHeight) + ypos,
- getSize().width, charHeight);
+ gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
+ charHeight);
gg.setColor(Color.white);
}
- else if (av.getSelectionGroup() != null &&
- av.getSelectionGroup().getSequences(null).contains(s))
+ else if (av.getSelectionGroup() != null
+ && av.getSelectionGroup().getSequences(null).contains(s))
{
gg.setColor(Color.lightGray);
- gg.fillRect(0, ( (i - starty) * charHeight) + ypos,
- getSize().width, charHeight);
+ gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
+ charHeight);
gg.setColor(Color.white);
}
else
{
gg.setColor(av.getSequenceColour(s));
- gg.fillRect(0, ( (i - starty) * charHeight) + ypos,
- getSize().width, charHeight);
+ gg.fillRect(0, ((i - starty) * charHeight) + ypos, getSize().width,
+ charHeight);
gg.setColor(Color.black);
}
gg.drawString(s.getDisplayId(av.getShowJVSuffix()), 0,
- ( (i - starty) * charHeight) + ypos +
- charHeight - (charHeight / 5));
+ ((i - starty) * charHeight) + ypos + charHeight
+ - (charHeight / 5));
- if (av.hasHiddenRows && av.showHiddenMarkers)
+ if (hiddenRows)
{
drawMarker(i, starty, ypos);
}
public void fastPaint(int vertical)
{
- if (gg == null)
+ if (gg == null || av.getWrapAlignment())
{
repaint();
return;
}
- gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical * av.charHeight);
+ ViewportRanges ranges = av.getRanges();
- int ss = av.startSeq, es = av.endSeq, transY = 0;
+ gg.copyArea(0, 0, getSize().width, imgHeight, 0,
+ -vertical * av.getCharHeight());
+
+ int ss = ranges.getStartSeq(), es = ranges.getEndSeq(), transY = 0;
if (vertical > 0) // scroll down
{
ss = es - vertical;
- if (ss < av.startSeq) // ie scrolling too fast, more than a page at a time
+ if (ss < ranges.getStartSeq()) // ie scrolling too fast, more than a page
+ // at a
+ // time
{
- ss = av.startSeq;
+ ss = ranges.getStartSeq();
}
else
{
- transY = imgHeight - vertical * av.charHeight;
+ transY = imgHeight - ((vertical + 1) * av.getCharHeight());
}
}
else if (vertical < 0)
{
es = ss - vertical;
- if (es > av.endSeq)
+ if (es > ranges.getEndSeq())
{
- es = av.endSeq;
+ es = ranges.getEndSeq();
}
}
repaint();
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
if (getSize().height < 0 || getSize().width < 0)
}
imgHeight = getSize().height;
- imgHeight -= imgHeight % av.charHeight;
+ imgHeight -= imgHeight % av.getCharHeight();
if (imgHeight < 1)
{
gg.setFont(av.getFont());
}
- //Fill in the background
+ // Fill in the background
gg.setColor(Color.white);
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,
- av.getFont().getSize());
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
+ .getFont().getSize());
gg.setFont(italic);
gg.fillRect(0, 0, getSize().width, getSize().height);
- drawIds(av.startSeq, av.endSeq);
+ drawIds(av.getRanges().getStartSeq(), av.getRanges().getEndSeq());
g.drawImage(image, 0, 0, this);
}
-
+
+ /**
+ * local copy of av.getCharHeight set at top of drawIds
+ */
+ private int avcharHeight;
+
void drawIds(int starty, int endy)
{
- Font italic = new Font(av.getFont().getName(), Font.ITALIC,
- av.getFont().getSize());
-
- gg.setFont(italic);
+ avcharHeight = av.getCharHeight();
Color currentColor = Color.white;
Color currentTextColor = Color.black;
+ final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+ || av.hasHiddenRows();
+ boolean hiddenRows = av.hasHiddenRows() && av.getShowHiddenMarkers();
+
if (av.getWrapAlignment())
{
- int maxwidth = av.alignment.getWidth();
- int alheight = av.alignment.getHeight();
+ drawIdsWrapped(starty, doHiddenCheck, hiddenRows);
+ return;
+ }
- if (av.hasHiddenColumns)
+ // Now draw the id strings
+ SequenceI seq;
+ for (int i = starty; i <= endy; i++)
+ {
+ seq = av.getAlignment().getSequenceAt(i);
+ if (seq == null)
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ continue;
}
-
- int annotationHeight = 0;
- AnnotationLabels labels = null;
-
- if (av.showAnnotation)
+ // hardwired italic IDs in applet currently
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
+ .getFont().getSize());
+ gg.setFont(italic);
+ // boolean isrep=false;
+ if (doHiddenCheck)
{
- AnnotationPanel ap = new AnnotationPanel(av);
- annotationHeight = ap.adjustPanelHeight();
- labels = new AnnotationLabels(av);
+ // isrep =
+ setHiddenFont(seq);
}
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ // Selected sequence colours
+ if ((searchResults != null) && searchResults.contains(seq))
+ {
+ currentColor = Color.black;
+ currentTextColor = Color.white;
+ }
+ else if ((av.getSelectionGroup() != null)
+ && av.getSelectionGroup().getSequences(null).contains(seq))
+ {
+ currentColor = Color.lightGray;
+ currentTextColor = Color.black;
+ }
+ else
{
- hgap += av.charHeight;
+ currentColor = av.getSequenceColour(seq);
+ currentTextColor = Color.black;
}
- int cHeight = alheight * av.charHeight
- + hgap
- + annotationHeight;
+ gg.setColor(currentColor);
+ // TODO: isrep could be used to highlight the representative in a
+ // different way
+ gg.fillRect(0, (i - starty) * avcharHeight, getSize().width,
+ avcharHeight);
+ gg.setColor(currentTextColor);
- int rowSize = av.getEndRes() - av.getStartRes();
+ gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), 0,
+ (((i - starty) * avcharHeight) + avcharHeight)
+ - (avcharHeight / 5));
- // Draw the rest of the panels
- for (int ypos = hgap, row = av.startRes;
- (ypos <= getSize().height) && (row < maxwidth);
- ypos += cHeight, row += rowSize)
+ if (hiddenRows)
{
- for (int i = starty; i < alheight; i++)
- {
+ drawMarker(i, starty, 0);
+ }
+ }
+ }
- SequenceI s = av.alignment.getSequenceAt(i);
- gg.setFont(italic);
- if (av.hasHiddenRows)
- {
- setHiddenFont(s);
- }
- drawIdString(gg, s, i, 0, ypos);
- }
+ /**
+ * Draws sequence ids in wrapped mode
+ *
+ * @param starty
+ * @param doHiddenCheck
+ * @param hiddenRows
+ */
+ protected void drawIdsWrapped(int starty, final boolean doHiddenCheck,
+ boolean hiddenRows)
+ {
+ int maxwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight();
- if (labels != null)
- {
- gg.translate(0, ypos + (alheight * av.charHeight));
- labels.drawComponent(gg, getSize().width);
- gg.translate(0, -ypos - (alheight * av.charHeight));
- }
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .findColumnPosition(maxwidth) - 1;
+ }
- }
+ int annotationHeight = 0;
+ AnnotationLabels labels = null;
+
+ if (av.isShowAnnotation())
+ {
+ AnnotationPanel ap = new AnnotationPanel(av);
+ annotationHeight = ap.adjustPanelHeight();
+ labels = new AnnotationLabels(av);
}
- else
+ int hgap = avcharHeight;
+ if (av.getScaleAboveWrapped())
{
- //Now draw the id strings
- SequenceI seq;
- for (int i = starty; i < endy; i++)
- {
+ hgap += avcharHeight;
+ }
- seq = av.alignment.getSequenceAt(i);
- if (seq == null)
- {
- continue;
- }
- gg.setFont(italic);
- //boolean isrep=false;
- if (av.hasHiddenRows)
- {
- //isrep =
- setHiddenFont(seq);
- }
+ int cHeight = alheight * avcharHeight + hgap + annotationHeight;
- // Selected sequence colours
- if ( (searchResults != null) &&
- searchResults.contains(seq))
- {
- currentColor = Color.black;
- currentTextColor = Color.white;
- }
- else if ( (av.getSelectionGroup() != null) &&
- av.getSelectionGroup().getSequences(null).contains(seq))
- {
- currentColor = Color.lightGray;
- currentTextColor = Color.black;
- }
- else
- {
- currentColor = av.getSequenceColour(seq);
- currentTextColor = Color.black;
- }
+ int rowSize = av.getRanges().getViewportWidth();
- gg.setColor(currentColor);
- // TODO: isrep could be used to highlight the representative in a different way
- gg.fillRect(0, (i - starty) * av.charHeight, getSize().width,
- av.charHeight);
- gg.setColor(currentTextColor);
+ // hardwired italic IDs in applet currently
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
+ .getFont().getSize());
+ gg.setFont(italic);
- gg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
- 0,
- ( ( (i - starty) * av.charHeight) + av.charHeight) -
- (av.charHeight / 5));
+ /*
+ * draw repeating sequence ids until out of sequence data or
+ * out of visible space, whichever comes first
+ */
+ int ypos = hgap;
+ int row = av.getRanges().getStartRes();
+ while ((ypos <= getHeight()) && (row < maxwidth))
+ {
+ for (int i = starty; i < alheight; i++)
+ {
- if (av.hasHiddenRows && av.showHiddenMarkers)
+ SequenceI s = av.getAlignment().getSequenceAt(i);
+ // gg.setFont(italic);
+ if (doHiddenCheck)
{
- drawMarker(i, starty, 0);
+ setHiddenFont(s);
}
+ drawIdString(gg, hiddenRows, s, i, 0, ypos);
+ }
+
+ if (labels != null)
+ {
+ gg.translate(0, ypos + (alheight * avcharHeight));
+ labels.drawComponent(gg, getSize().width);
+ gg.translate(0, -ypos - (alheight * avcharHeight));
}
+ ypos += cHeight;
+ row += rowSize;
}
}
- public void setHighlighted(java.util.Vector found)
+ public void setHighlighted(List<SequenceI> list)
{
- searchResults = found;
+ searchResults = list;
repaint();
}
void drawMarker(int i, int starty, int yoffset)
{
- SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences;
- //Use this method here instead of calling hiddenSeq adjust
- //3 times.
+ SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
+ // Use this method here instead of calling hiddenSeq adjust
+ // 3 times.
int hSize = hseqs.length;
int hiddenIndex = i;
int lastIndex = i - 1;
int nextIndex = i + 1;
-
for (int j = 0; j < hSize; j++)
{
if (hseqs[j] != null)
gg.setColor(Color.blue);
if (below)
{
- gg.fillPolygon(new int[]
- {getSize().width - av.charHeight,
- getSize().width - av.charHeight,
- getSize().width},
- new int[]
- {
- (i - starty) * av.charHeight + yoffset,
- (i - starty) * av.charHeight + yoffset + av.charHeight / 4,
- (i - starty) * av.charHeight + yoffset
- }, 3);
+ gg.fillPolygon(new int[] { getSize().width - avcharHeight,
+ getSize().width - avcharHeight, getSize().width }, new int[] {
+ (i - starty) * avcharHeight + yoffset,
+ (i - starty) * avcharHeight + yoffset + avcharHeight / 4,
+ (i - starty) * avcharHeight + yoffset }, 3);
}
if (above)
{
- gg.fillPolygon(new int[]
- {getSize().width - av.charHeight,
- getSize().width - av.charHeight,
- getSize().width},
- new int[]
- {
- (i - starty + 1) * av.charHeight + yoffset,
- (i - starty + 1) * av.charHeight + yoffset -
- av.charHeight / 4,
- (i - starty + 1) * av.charHeight + yoffset
- }, 3);
+ gg.fillPolygon(new int[] { getSize().width - avcharHeight,
+ getSize().width - avcharHeight, getSize().width }, new int[] {
+ (i - starty + 1) * avcharHeight + yoffset,
+ (i - starty + 1) * avcharHeight + yoffset - avcharHeight / 4,
+ (i - starty + 1) * avcharHeight + yoffset }, 3);
}
}
+
boolean setHiddenFont(SequenceI seq)
{
- Font bold = new Font(av.getFont().getName(), Font.BOLD
- ,
- av.getFont().getSize());
+ Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
+ .getSize());
- if (av.hiddenRepSequences != null &&
- av.hiddenRepSequences.containsKey(seq))
+ if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq))
{
gg.setFont(bold);
return true;
}
return false;
}
+
+ /**
+ * Respond to viewport range changes (e.g. alignment panel was scrolled). Both
+ * scrolling and resizing change viewport ranges. Scrolling changes both start
+ * and end points, but resize only changes end values. Here we only want to
+ * fastpaint on a scroll, with resize using a normal paint, so scroll events
+ * are identified as changes to the horizontal or vertical start value.
+ * <p>
+ * In unwrapped mode, only responds to a vertical scroll, as horizontal scroll
+ * leaves sequence ids unchanged. In wrapped mode, only vertical scroll is
+ * provided, but it generates a change of "startres" which does require an
+ * update here.
+ */
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ String propertyName = evt.getPropertyName();
+ if (propertyName.equals(ViewportRanges.STARTSEQ)
+ || (av.getWrapAlignment() && propertyName
+ .equals(ViewportRanges.STARTRES)))
+ {
+ fastPaint((int) evt.getNewValue() - (int) evt.getOldValue());
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff