X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=7689535dcf747428206d0af5025d71fd02264abf;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=2dceac5e634d01cef811fc60ff183dbe01dd8bc3;hpb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;p=jalview.git
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 2dceac5..7689535 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -1,25 +1,36 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.viewmodel.AlignmentViewport;
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
public class SeqCanvas extends Panel
{
@@ -51,9 +62,18 @@ public class SeqCanvas extends Panel
fr = new FeatureRenderer(av);
sr = new SequenceRenderer(av);
PaintRefresher.Register(this, av.getSequenceSetId());
+ updateViewport();
+ }
+
+ int avcharHeight = 0, avcharWidth = 0;
+
+ private void updateViewport()
+ {
+ avcharHeight = av.getCharHeight();
+ avcharWidth = av.getCharWidth();
}
- public AlignViewport getViewport()
+ public AlignmentViewport getViewport()
{
return av;
}
@@ -68,7 +88,7 @@ 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;
@@ -83,20 +103,20 @@ public class SeqCanvas extends Panel
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) * avcharWidth,
+ ypos - (avcharHeight / 2));
- g.drawLine(((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
- (ypos + 2) - (av.charHeight / 2),
- ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
+ g.drawLine(((i - startx - 1) * avcharWidth) + (avcharWidth / 2),
+ (ypos + 2) - (avcharHeight / 2),
+ ((i - startx - 1) * 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;
+ ypos += avcharHeight;
if (av.hasHiddenColumns())
{
startx = av.getColumnSelection().adjustForHiddenColumns(startx);
@@ -133,16 +153,16 @@ 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())
{
@@ -173,8 +193,8 @@ 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));
}
}
}
@@ -188,6 +208,8 @@ public class SeqCanvas extends Panel
return;
}
+ updateViewport();
+
// Its possible on certain browsers that the call to fastpaint
// is faster than it can paint, so this check here catches
// this possibility
@@ -199,16 +221,16 @@ public class SeqCanvas extends Panel
lastsr = av.startRes;
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;
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)
@@ -225,7 +247,7 @@ public class SeqCanvas extends Panel
}
else
{
- transY = imgHeight - vertical * av.charHeight;
+ transY = imgHeight - vertical * avcharHeight;
}
}
else if (vertical < 0)
@@ -259,6 +281,7 @@ public class SeqCanvas extends Panel
paint(g);
}
+ @Override
public void paint(Graphics g)
{
@@ -278,12 +301,13 @@ 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)
{
@@ -318,24 +342,24 @@ 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();
}
/**
@@ -365,31 +389,31 @@ 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)
+ 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);
@@ -416,12 +440,12 @@ 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);
@@ -430,11 +454,11 @@ 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())
{
g.setColor(Color.blue);
int res;
@@ -449,25 +473,24 @@ public class SeqCanvas extends Panel
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 * 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);
g.setClip(null);
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
g.translate(0, cHeight + ypos + 4);
if (annotations == null)
@@ -491,7 +514,7 @@ public class SeqCanvas extends Panel
int getAnnotationHeight()
{
- if (!av.showAnnotation)
+ if (!av.isShowAnnotation())
{
return 0;
}
@@ -504,59 +527,61 @@ 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, int startRes, int endRes,
+ int startSeq, int endSeq, int offset)
{
+
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;
- for (int i = 0; i < regions.size(); i++)
+ if (av.hasHiddenColumns())
{
- int[] region = (int[]) regions.elementAt(i);
- int hideStart = region[0];
- int hideEnd = region[1];
-
- if (hideStart <= blockStart)
+ for (int[] region : av.getColumnSelection().getHiddenColumns())
{
- blockStart += (hideEnd - hideStart) + 1;
- continue;
- }
+ int hideStart = region[0];
+ int hideEnd = region[1];
- blockEnd = hideStart - 1;
+ if (hideStart <= blockStart)
+ {
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
- g1.translate(screenY * av.charWidth, 0);
+ blockEnd = hideStart - 1;
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+ g1.translate(screenY * avcharWidth, 0);
- if (av.getShowHiddenMarkers())
- {
- 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);
- }
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
- g1.translate(-screenY * av.charWidth, 0);
- screenY += blockEnd - blockStart + 1;
- blockStart = hideEnd + 1;
- }
+ if (av.getShowHiddenMarkers())
+ {
+ g1.setColor(Color.blue);
+ g1.drawLine((blockEnd - blockStart + 1) * avcharWidth - 1,
+ 0 + offset, (blockEnd - blockStart + 1) * avcharWidth
+ - 1, (endSeq - startSeq) * avcharHeight
+ + offset);
+ }
+ 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);
+ g1.translate(screenY * avcharWidth, 0);
draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
- g1.translate(-screenY * av.charWidth, 0);
+ g1.translate(-screenY * avcharWidth, 0);
}
}
@@ -568,8 +593,8 @@ 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
@@ -584,12 +609,12 @@ public class SeqCanvas extends Panel
}
sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
- startRes, endRes, offset + ((i - startSeq) * av.charHeight));
+ startRes, endRes, offset + ((i - startSeq) * avcharHeight));
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
fr.drawSequence(g, nextSeq, startRes, endRes, offset
- + ((i - startSeq) * av.charHeight));
+ + ((i - startSeq) * avcharHeight));
}
// / Highlight search Results once all sequences have been drawn
@@ -604,8 +629,8 @@ public class SeqCanvas extends Panel
{
sr.drawHighlightedText(nextSeq, visibleResults[r],
visibleResults[r + 1], (visibleResults[r] - startRes)
- * av.charWidth, offset
- + ((i - startSeq) * av.charHeight));
+ * avcharWidth, offset
+ + ((i - startSeq) * avcharHeight));
}
}
}
@@ -613,9 +638,8 @@ 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));
+ sr.drawCursor(nextSeq, cursorX, (cursorX - startRes) * avcharWidth,
+ offset + ((i - startSeq) * avcharHeight));
}
}
@@ -627,7 +651,7 @@ public class SeqCanvas extends Panel
}
- void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
+ private void drawGroupsBoundaries(Graphics g, int startRes, int endRes,
int startSeq, int endSeq, int offset)
{
//
@@ -643,7 +667,7 @@ public class SeqCanvas extends Panel
if ((group == null) && (av.getAlignment().getGroups().size() > 0))
{
- group = (SequenceGroup) av.getAlignment().getGroups().get(0);
+ group = av.getAlignment().getGroups().get(0);
groupIndex = 0;
}
@@ -660,16 +684,16 @@ public class SeqCanvas extends Panel
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)
+ if ((sx <= (endRes - startRes) * avcharWidth)
&& group.getSequences(null).contains(
av.getAlignment().getSequenceAt(i)))
{
@@ -678,7 +702,7 @@ public class SeqCanvas extends Panel
.contains(
av.getAlignment().getSequenceAt(i + 1))))
{
- bottom = sy + av.charHeight;
+ bottom = sy + avcharHeight;
}
if (!inGroup)
@@ -728,9 +752,9 @@ 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)
@@ -752,7 +776,7 @@ 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);
@@ -773,9 +797,9 @@ 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)
@@ -800,8 +824,7 @@ public class SeqCanvas extends Panel
break;
}
- group = (SequenceGroup) av.getAlignment().getGroups()
- .get(groupIndex);
+ group = av.getAlignment().getGroups().get(groupIndex);
} while (groupIndex < av.getAlignment().getGroups().size());
}