X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=735046ea57efb40fbf734b70f3241d02ee192c18;hb=eb2e3276b62ef033703f9b55bbddfdff3fe384df;hp=fd9d76803eabcc46240236c46524f73b46f9b9b4;hpb=8a6fa9ea9900d0f106529c3f6283e7f9d76dd2cb;p=jalview.git
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index fd9d768..735046e 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -1,27 +1,47 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.awt.*;
-
-import jalview.datamodel.*;
-
-public class SeqCanvas extends Panel
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.VisibleContigsIterator;
+import jalview.renderer.ScaleRenderer;
+import jalview.renderer.ScaleRenderer.ScaleMark;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.beans.PropertyChangeEvent;
+import java.util.Iterator;
+
+@SuppressWarnings("serial")
+public class SeqCanvas extends Panel implements ViewportListenerI
{
FeatureRenderer fr;
@@ -37,8 +57,6 @@ public class SeqCanvas extends Panel
AlignViewport av;
- SearchResults searchResults = null;
-
boolean fastPaint = false;
int cursorX = 0;
@@ -51,9 +69,20 @@ public class SeqCanvas extends Panel
fr = new FeatureRenderer(av);
sr = new SequenceRenderer(av);
PaintRefresher.Register(this, av.getSequenceSetId());
+ updateViewport();
+
+ av.getRanges().addPropertyChangeListener(this);
+ }
+
+ int avcharHeight = 0, avcharWidth = 0;
+
+ private void updateViewport()
+ {
+ avcharHeight = av.getCharHeight();
+ avcharWidth = av.getCharWidth();
}
- public AlignViewport getViewport()
+ public AlignmentViewport getViewport()
{
return av;
}
@@ -68,51 +97,50 @@ public class SeqCanvas extends Panel
return sr;
}
- void drawNorthScale(Graphics g, int startx, int endx, int ypos)
+ private void drawNorthScale(Graphics g, int startx, int endx, int ypos)
{
- int scalestartx = startx - startx % 10 + 10;
-
+ updateViewport();
g.setColor(Color.black);
-
- // NORTH SCALE
- for (int i = scalestartx; i < endx; i += 10)
+ for (ScaleMark mark : new ScaleRenderer().calculateMarks(av, startx,
+ endx))
{
- int value = i;
- if (av.hasHiddenColumns)
+ int mpos = mark.column; // (i - startx - 1)
+ if (mpos < 0)
{
- value = av.getColumnSelection().adjustForHiddenColumns(value);
+ continue;
}
+ String mstring = mark.text;
- g.drawString(String.valueOf(value), (i - startx - 1) * av.charWidth,
- ypos - (av.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);
+ if (mark.major)
+ {
+ if (mstring != null)
+ {
+ g.drawString(mstring, mpos * avcharWidth,
+ ypos - (avcharHeight / 2));
+ }
+ g.drawLine((mpos * avcharWidth) + (avcharWidth / 2),
+ (ypos + 2) - (avcharHeight / 2),
+ (mpos * avcharWidth) + (avcharWidth / 2), ypos - 2);
+ }
}
}
- void drawWestScale(Graphics g, int startx, int endx, int ypos)
+ private void drawWestScale(Graphics g, int startx, int endx, int ypos)
{
FontMetrics fm = getFontMetrics(av.getFont());
- ypos += av.charHeight;
- if (av.hasHiddenColumns)
+ ypos += avcharHeight;
+ if (av.hasHiddenColumns())
{
- startx = av.getColumnSelection().adjustForHiddenColumns(startx);
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
- }
-
- int maxwidth = av.alignment.getWidth();
- if (av.hasHiddenColumns)
- {
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ startx = av.getAlignment().getHiddenColumns()
+ .visibleToAbsoluteColumn(startx);
+ endx = av.getAlignment().getHiddenColumns()
+ .visibleToAbsoluteColumn(endx);
}
// WEST SCALE
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
- SequenceI seq = av.alignment.getSequenceAt(i);
+ SequenceI seq = av.getAlignment().getSequenceAt(i);
int index = startx;
int value = -1;
@@ -125,7 +153,7 @@ public class SeqCanvas extends Panel
continue;
}
- value = av.alignment.getSequenceAt(i).findPosition(index);
+ value = av.getAlignment().getSequenceAt(i).findPosition(index);
break;
}
@@ -133,27 +161,28 @@ public class SeqCanvas extends Panel
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));
+ - avcharWidth / 2;
+ g.drawString(value + "", x,
+ (ypos + (i * avcharHeight)) - (avcharHeight / 5));
}
}
}
- void drawEastScale(Graphics g, int startx, int endx, int ypos)
+ private void drawEastScale(Graphics g, int startx, int endx, int ypos)
{
- ypos += av.charHeight;
+ ypos += avcharHeight;
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
- endx = av.getColumnSelection().adjustForHiddenColumns(endx);
+ endx = av.getAlignment().getHiddenColumns()
+ .visibleToAbsoluteColumn(endx);
}
SequenceI seq;
// EAST SCALE
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
- seq = av.alignment.getSequenceAt(i);
+ seq = av.getAlignment().getSequenceAt(i);
int index = endx;
int value = -1;
@@ -173,8 +202,8 @@ public class SeqCanvas extends Panel
if (value != -1)
{
- g.drawString(String.valueOf(value), 0, (ypos + (i * av.charHeight))
- - (av.charHeight / 5));
+ g.drawString(String.valueOf(value), 0,
+ (ypos + (i * avcharHeight)) - (avcharHeight / 5));
}
}
}
@@ -188,27 +217,33 @@ public class SeqCanvas extends Panel
return;
}
+ ViewportRanges ranges = av.getRanges();
+
+ updateViewport();
+
// Its possible on certain browsers that the call to fastpaint
// is faster than it can paint, so this check here catches
// this possibility
- if (lastsr + horizontal != av.startRes)
+ if (lastsr + horizontal != ranges.getStartRes())
{
- horizontal = av.startRes - lastsr;
+ horizontal = ranges.getStartRes() - lastsr;
}
- lastsr = av.startRes;
+ lastsr = ranges.getStartRes();
fastPaint = true;
- gg.copyArea(horizontal * av.charWidth, vertical * av.charHeight,
- imgWidth - horizontal * av.charWidth, imgHeight - vertical
- * av.charHeight, -horizontal * av.charWidth, -vertical
- * av.charHeight);
+ gg.copyArea(horizontal * avcharWidth, vertical * avcharHeight,
+ imgWidth - horizontal * avcharWidth,
+ imgHeight - vertical * avcharHeight, -horizontal * avcharWidth,
+ -vertical * avcharHeight);
- int sr = av.startRes, er = av.endRes, ss = av.startSeq, es = av.endSeq, transX = 0, transY = 0;
+ int sr = ranges.getStartRes(), er = ranges.getEndRes(),
+ ss = ranges.getStartSeq(), es = ranges.getEndSeq(), transX = 0,
+ transY = 0;
if (horizontal > 0) // scrollbar pulled right, image to the left
{
- transX = (er - sr - horizontal) * av.charWidth;
+ transX = (er - sr - horizontal) * avcharWidth;
sr = er - horizontal;
}
else if (horizontal < 0)
@@ -219,21 +254,23 @@ public class SeqCanvas extends Panel
else 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) * avcharHeight);
}
}
else if (vertical < 0)
{
es = ss - vertical;
- if (es > av.endSeq)
+ if (es > ranges.getEndSeq())
{
- es = av.endSeq;
+ es = ranges.getEndSeq();
}
}
@@ -254,17 +291,19 @@ public class SeqCanvas extends Panel
* at 0). NOTE 1: The av limits are set in setFont in this class and in the
* adjustment listener in SeqPanel when the scrollbars move.
*/
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
if (img != null
- && (fastPaint || (getSize().width != g.getClipBounds().width) || (getSize().height != g
- .getClipBounds().height)))
+ && (fastPaint || (getSize().width != g.getClipBounds().width)
+ || (getSize().height != g.getClipBounds().height)))
{
g.drawImage(img, 0, 0, this);
fastPaint = false;
@@ -278,12 +317,13 @@ public class SeqCanvas extends Panel
return;
}
+ updateViewport();
// this draws the whole of the alignment
imgWidth = this.getSize().width;
imgHeight = this.getSize().height;
- imgWidth -= imgWidth % av.charWidth;
- imgHeight -= imgHeight % av.charHeight;
+ imgWidth -= imgWidth % avcharWidth;
+ imgHeight -= imgHeight % avcharHeight;
if (imgWidth < 1 || imgHeight < 1)
{
@@ -301,13 +341,16 @@ public class SeqCanvas extends Panel
gg.setColor(Color.white);
gg.fillRect(0, 0, imgWidth, imgHeight);
+ ViewportRanges ranges = av.getRanges();
+
if (av.getWrapAlignment())
{
- drawWrappedPanel(gg, imgWidth, imgHeight, av.startRes);
+ drawWrappedPanel(gg, imgWidth, imgHeight, ranges.getStartRes());
}
else
{
- drawPanel(gg, av.startRes, av.endRes, av.startSeq, av.endSeq, 0);
+ drawPanel(gg, ranges.getStartRes(), ranges.getEndRes(),
+ ranges.getStartSeq(), ranges.getEndSeq(), 0);
}
g.drawImage(img, 0, 0, this);
@@ -318,24 +361,24 @@ public class SeqCanvas extends Panel
public int getWrappedCanvasWidth(int cwidth)
{
- cwidth -= cwidth % av.charWidth;
+ cwidth -= cwidth % av.getCharWidth();
FontMetrics fm = getFontMetrics(av.getFont());
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) / av.getCharWidth();
}
/**
@@ -348,9 +391,10 @@ public class SeqCanvas extends Panel
String mask = "0";
int maxWidth = 0;
int tmp;
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ AlignmentI alignment = av.getAlignment();
+ for (int i = 0; i < alignment.getHeight(); i++)
{
- tmp = av.alignment.getSequenceAt(i).getEnd();
+ tmp = alignment.getSequenceAt(i).getEnd();
if (tmp > maxWidth)
{
maxWidth = tmp;
@@ -364,45 +408,43 @@ public class SeqCanvas extends Panel
return mask;
}
- public void drawWrappedPanel(Graphics g, int canvasWidth,
+ private void drawWrappedPanel(Graphics g, int canvasWidth,
int canvasHeight, int startRes)
{
AlignmentI al = av.getAlignment();
FontMetrics fm = getFontMetrics(av.getFont());
- if (av.scaleRightWrapped)
+ LABEL_EAST = 0;
+ LABEL_WEST = 0;
+
+ 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 = avcharHeight;
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += avcharHeight;
}
- int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / av.charWidth;
- int cHeight = av.getAlignment().getHeight() * av.charHeight;
+ int cWidth = (canvasWidth - LABEL_EAST - LABEL_WEST) / avcharWidth;
+ int cHeight = av.getAlignment().getHeight() * avcharHeight;
av.setWrappedWidth(cWidth);
- av.endRes = av.startRes + cWidth;
+ av.getRanges().setViewportStartAndWidth(startRes, cWidth);
int endx;
int ypos = hgap;
- int maxwidth = av.alignment.getWidth() - 1;
-
- if (av.hasHiddenColumns)
- {
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
- }
+ int maxwidth = av.getAlignment().getVisibleWidth();
while ((ypos <= canvasHeight) && (startRes < maxwidth))
{
@@ -415,12 +457,12 @@ public class SeqCanvas extends Panel
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);
@@ -429,44 +471,41 @@ public class SeqCanvas extends Panel
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())
{
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
g.setColor(Color.blue);
int res;
- for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
- .size(); i++)
+ Iterator it = hidden.getStartRegionIterator(startRes,
+ endx + 1);
+ while (it.hasNext())
{
- res = av.getColumnSelection().findHiddenRegionPosition(i)
- - startRes;
-
- if (res < 0 || res > endx - startRes)
- {
- continue;
- }
-
- gg.fillPolygon(new int[]
- { res * av.charWidth - av.charHeight / 4,
- res * av.charWidth + av.charHeight / 4, res * av.charWidth },
+ res = it.next() - startRes;
+ gg.fillPolygon(
new int[]
- { ypos - (av.charHeight / 2), ypos - (av.charHeight / 2),
- ypos - (av.charHeight / 2) + 8 }, 3);
-
+ { res * avcharWidth - avcharHeight / 4,
+ res * avcharWidth + avcharHeight / 4,
+ res * avcharWidth },
+ new int[]
+ { ypos - (avcharHeight / 2), ypos - (avcharHeight / 2),
+ ypos - (avcharHeight / 2) + 8 },
+ 3);
}
}
if (g.getClip() == null)
{
- g.setClip(0, 0, cWidth * av.charWidth, canvasHeight);
+ g.setClip(0, 0, cWidth * avcharWidth, canvasHeight);
}
- drawPanel(g, startRes, endx, 0, al.getHeight(), ypos);
+ drawPanel(g, startRes, endx, 0, al.getHeight() - 1, ypos);
g.setClip(null);
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
g.translate(0, cHeight + ypos + 4);
if (annotations == null)
@@ -490,7 +529,7 @@ public class SeqCanvas extends Panel
int getAnnotationHeight()
{
- if (!av.showAnnotation)
+ if (!av.isShowAnnotation())
{
return 0;
}
@@ -503,62 +542,55 @@ public class SeqCanvas extends Panel
return annotations.adjustPanelHeight();
}
- void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
- int endSeq, int offset)
+ private void drawPanel(Graphics g1, final int startRes, final int endRes,
+ final int startSeq, final int endSeq, final int offset)
{
- if (!av.hasHiddenColumns)
+
+ if (!av.hasHiddenColumns())
{
draw(g1, startRes, endRes, startSeq, endSeq, offset);
}
else
{
- java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
-
int screenY = 0;
- int blockStart = startRes;
- int blockEnd = endRes;
+ int blockStart;
+ int blockEnd;
- for (int i = 0; i < regions.size(); i++)
- {
- int[] region = (int[]) regions.elementAt(i);
- int hideStart = region[0];
- int hideEnd = region[1];
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ VisibleContigsIterator regions = hidden
+ .getVisContigsIterator(startRes, endRes + 1, true);
- if (hideStart <= blockStart)
- {
- blockStart += (hideEnd - hideStart) + 1;
- continue;
- }
-
- blockEnd = hideStart - 1;
+ while (regions.hasNext())
+ {
+ int[] region = regions.next();
+ blockEnd = region[1];
+ blockStart = region[0];
- g1.translate(screenY * av.charWidth, 0);
+ /*
+ * draw up to just before the next hidden region, or the end of
+ * the visible region, whichever comes first
+ */
+ g1.translate(screenY * avcharWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
- if (av.getShowHiddenMarkers())
+ /*
+ * draw the downline of the hidden column marker (ScalePanel draws the
+ * triangle on top) if we reached it
+ */
+ if (av.getShowHiddenMarkers()
+ && (regions.hasNext() || regions.endsAtHidden()))
{
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) * avcharWidth - 1,
+ 0 + offset, (blockEnd - blockStart + 1) * avcharWidth - 1,
+ (endSeq - startSeq + 1) * avcharHeight + offset);
}
- g1.translate(-screenY * av.charWidth, 0);
+ g1.translate(-screenY * avcharWidth, 0);
screenY += blockEnd - blockStart + 1;
- blockStart = hideEnd + 1;
- }
-
- if (screenY <= (endRes - startRes))
- {
- blockEnd = blockStart + (endRes - startRes) - screenY;
- g1.translate(screenY * av.charWidth, 0);
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
-
- g1.translate(-screenY * av.charWidth, 0);
}
}
-
}
// int startRes, int endRes, int startSeq, int endSeq, int x, int y,
@@ -567,44 +599,44 @@ public class SeqCanvas extends Panel
int offset)
{
g.setFont(av.getFont());
- sr.prepare(g, av.renderGaps);
-
+ sr.prepare(g, av.isRenderGaps());
+ updateViewport();
SequenceI nextSeq;
// / First draw the sequences
// ///////////////////////////
- for (int i = startSeq; i < endSeq; i++)
+ for (int i = startSeq; i <= endSeq; i++)
{
- nextSeq = av.alignment.getSequenceAt(i);
+ nextSeq = av.getAlignment().getSequenceAt(i);
if (nextSeq == null)
{
continue;
}
- sr.drawSequence(nextSeq, av.alignment.findAllGroups(nextSeq),
- startRes, endRes, offset + ((i - startSeq) * av.charHeight));
+ sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
+ startRes, endRes, offset + ((i - startSeq) * avcharHeight));
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
- fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * av.charHeight));
+ fr.drawSequence(g, nextSeq, startRes, endRes,
+ offset + ((i - startSeq) * avcharHeight), false);
}
// / Highlight search Results once all sequences have been drawn
// ////////////////////////////////////////////////////////
- if (searchResults != null)
+ if (av.hasSearchResults())
{
- int[] visibleResults = searchResults.getResults(nextSeq, startRes,
- endRes);
+ int[] visibleResults = av.getSearchResults().getResults(nextSeq,
+ startRes, endRes);
if (visibleResults != null)
{
for (int r = 0; r < visibleResults.length; r += 2)
{
sr.drawHighlightedText(nextSeq, visibleResults[r],
- visibleResults[r + 1], (visibleResults[r] - startRes)
- * av.charWidth, offset
- + ((i - startSeq) * av.charHeight));
+ visibleResults[r + 1],
+ (visibleResults[r] - startRes) * avcharWidth,
+ offset + ((i - startSeq) * avcharHeight));
}
}
}
@@ -612,21 +644,22 @@ public class SeqCanvas extends Panel
if (av.cursorMode && cursorY == i && cursorX >= startRes
&& cursorX <= endRes)
{
- sr.drawCursor(nextSeq, cursorX,
- (cursorX - startRes) * av.charWidth, offset
- + ((i - startSeq) * av.charHeight));
+ char s = nextSeq.getCharAt(cursorX);
+
+ sr.drawCursor(g,s, (cursorX - startRes) * avcharWidth,
+ offset + ((i - startSeq) * avcharHeight));
}
}
if (av.getSelectionGroup() != null
- || av.alignment.getGroups().size() > 0)
+ || av.getAlignment().getGroups().size() > 0)
{
drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
}
}
- void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
+ private void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
int startSeq, int endSeq, int offset)
{
//
@@ -640,9 +673,9 @@ public class SeqCanvas extends Panel
int ex = -1;
int groupIndex = -1;
- if ((group == null) && (av.alignment.getGroups().size() > 0))
+ if ((group == null) && (av.getAlignment().getGroups().size() > 0))
{
- group = (SequenceGroup) av.alignment.getGroups().elementAt(0);
+ group = av.getAlignment().getGroups().get(0);
groupIndex = 0;
}
@@ -655,35 +688,35 @@ public class SeqCanvas extends Panel
boolean inGroup = false;
int top = -1;
int bottom = -1;
- int alHeight = av.alignment.getHeight() - 1;
+ int alHeight = av.getAlignment().getHeight() - 1;
- for (i = startSeq; i < endSeq; i++)
+ 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) * avcharWidth;
+ sy = offset + ((i - startSeq) * avcharHeight);
+ ex = (((group.getEndRes() + 1) - group.getStartRes())
+ * avcharWidth) - 1;
if (sx + ex < 0 || sx > imgWidth)
{
continue;
}
- if ((sx <= (endRes - startRes) * av.charWidth)
- && group.getSequences(null).contains(
- av.alignment.getSequenceAt(i)))
+ if ((sx <= (endRes - startRes) * avcharWidth)
+ && group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i)))
{
if ((bottom == -1)
- && (i >= alHeight || !group.getSequences(null)
- .contains(av.alignment.getSequenceAt(i + 1))))
+ && (i >= alHeight || !group.getSequences(null).contains(
+ av.getAlignment().getSequenceAt(i + 1))))
{
- bottom = sy + av.charHeight;
+ bottom = sy + avcharHeight;
}
if (!inGroup)
{
- if (((top == -1) && (i == 0))
- || !group.getSequences(null).contains(
- av.alignment.getSequenceAt(i - 1)))
+ if (((top == -1) && (i == 0)) || !group.getSequences(null)
+ .contains(av.getAlignment().getSequenceAt(i - 1)))
{
top = sy;
}
@@ -726,9 +759,9 @@ public class SeqCanvas extends Panel
ex = imgWidth;
}
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+ else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
{
- ex = (endRes - startRes + 1) * av.charWidth;
+ ex = (endRes - startRes + 1) * avcharWidth;
}
if (top != -1)
@@ -750,7 +783,7 @@ public class SeqCanvas extends Panel
if (inGroup)
{
- sy = offset + ((i - startSeq) * av.charHeight);
+ sy = offset + ((i - startSeq) * avcharHeight);
if (sx >= 0 && sx < imgWidth)
{
g.drawLine(sx, oldY, sx, sy);
@@ -771,9 +804,9 @@ public class SeqCanvas extends Panel
{
ex = imgWidth;
}
- else if (sx + ex >= (endRes - startRes + 1) * av.charWidth)
+ else if (sx + ex >= (endRes - startRes + 1) * avcharWidth)
{
- ex = (endRes - startRes + 1) * av.charWidth;
+ ex = (endRes - startRes + 1) * avcharWidth;
}
if (top != -1)
@@ -793,23 +826,105 @@ public class SeqCanvas extends Panel
groupIndex++;
- if (groupIndex >= av.alignment.getGroups().size())
+ if (groupIndex >= av.getAlignment().getGroups().size())
{
break;
}
- group = (SequenceGroup) av.alignment.getGroups().elementAt(
- groupIndex);
- } while (groupIndex < av.alignment.getGroups().size());
+ group = av.getAlignment().getGroups().get(groupIndex);
+ } while (groupIndex < av.getAlignment().getGroups().size());
}
}
- public void highlightSearchResults(SearchResults results)
+ public void highlightSearchResults(SearchResultsI results)
{
- searchResults = results;
-
+ av.setSearchResults(results);
repaint();
}
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ String eventName = evt.getPropertyName();
+
+ if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
+ {
+ fastPaint = true;
+ repaint();
+ return;
+ }
+ else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT))
+ {
+ fastPaint = false;
+ repaint();
+ return;
+ }
+
+ if (!av.getWrapAlignment())
+ {
+ int scrollX = 0;
+ if (eventName.equals(ViewportRanges.STARTRES)
+ || eventName.equals(ViewportRanges.STARTRESANDSEQ))
+ {
+ // Make sure we're not trying to draw a panel
+ // larger than the visible window
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ scrollX = (int) evt.getNewValue() - (int) evt.getOldValue();
+ }
+ else
+ {
+ scrollX = ((int[]) evt.getNewValue())[0]
+ - ((int[]) evt.getOldValue())[0];
+ }
+ ViewportRanges vpRanges = av.getRanges();
+ int range = vpRanges.getEndRes() - vpRanges.getStartRes();
+ if (scrollX > range)
+ {
+ scrollX = range;
+ }
+ else if (scrollX < -range)
+ {
+ scrollX = -range;
+ }
+ }
+
+ // 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.
+ if (eventName.equals(ViewportRanges.STARTRES))
+ {
+ // scroll - startres and endres both change
+ fastPaint(scrollX, 0);
+ }
+ else if (eventName.equals(ViewportRanges.STARTSEQ))
+ {
+ // scroll
+ fastPaint(0, (int) evt.getNewValue() - (int) evt.getOldValue());
+ }
+ else if (eventName.equals(ViewportRanges.STARTRESANDSEQ))
+ {
+ fastPaint(scrollX, 0);
+ }
+ }
+ }
+
+ /**
+ * Ensure that a full paint is done next, for whatever reason. This was
+ * necessary for JavaScript; apparently in Java the timing is just right on
+ * multiple threads (EventQueue-0, Consensus, Conservation) that we can get
+ * away with one fast paint before the others, but this ensures that in the
+ * end we get a full paint. Problem arose in relation to copy/paste, where the
+ * paste was not finalized with a full paint.
+ *
+ * @author hansonr 2019.04.17
+ */
+ public void clearFastPaint()
+ {
+ fastPaint = false;
+ }
+
}