X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=58a4f107519548f27d3e5398983a05484f67f677;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=bec3c630439f7214f610f6295efec974dbdd63bc;hpb=67d05eb25eaeae54f1291ac2954305da266ad57b;p=jalview.git
diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index bec3c63..58a4f10 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,43 +1,53 @@
/*
- * 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 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.
- *
- * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.appletgui;
-import java.awt.*;
+import jalview.datamodel.SequenceI;
-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.util.List;
-public class IdCanvas
- extends Panel
+public class IdCanvas extends Panel
{
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 searchResults;
public IdCanvas(AlignViewport av)
{
@@ -46,39 +56,39 @@ public class IdCanvas
PaintRefresher.Register(this, av.getSequenceSetId());
}
- 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);
}
@@ -93,7 +103,8 @@ public class IdCanvas
return;
}
- gg.copyArea(0, 0, getSize().width, imgHeight, 0, -vertical * av.charHeight);
+ gg.copyArea(0, 0, getSize().width, imgHeight, 0,
+ -vertical * av.getCharHeight());
int ss = av.startSeq, es = av.endSeq, transY = 0;
if (vertical > 0) // scroll down
@@ -105,7 +116,7 @@ public class IdCanvas
}
else
{
- transY = imgHeight - vertical * av.charHeight;
+ transY = imgHeight - vertical * av.getCharHeight();
}
}
else if (vertical < 0)
@@ -146,7 +157,7 @@ public class IdCanvas
}
imgHeight = getSize().height;
- imgHeight -= imgHeight % av.charHeight;
+ imgHeight -= imgHeight % av.getCharHeight();
if (imgHeight < 1)
{
@@ -160,33 +171,45 @@ public class IdCanvas
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);
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());
+ // hardwired italic IDs in applet currently
+ Font italic = new Font(av.getFont().getName(), Font.ITALIC, av
+ .getFont().getSize());
+ // temp variable for speed
+ avcharHeight = av.getCharHeight();
gg.setFont(italic);
Color currentColor = Color.white;
Color currentTextColor = Color.black;
+ final boolean doHiddenCheck = av.isDisplayReferenceSeq()
+ || av.hasHiddenRows(), hiddenRows = av.hasHiddenRows()
+ && av.getShowHiddenMarkers();
+
if (av.getWrapAlignment())
{
- int maxwidth = av.alignment.getWidth();
- int alheight = av.alignment.getHeight();
+ int maxwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
@@ -194,80 +217,74 @@ public class IdCanvas
int annotationHeight = 0;
AnnotationLabels labels = null;
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
AnnotationPanel ap = new AnnotationPanel(av);
annotationHeight = ap.adjustPanelHeight();
labels = new AnnotationLabels(av);
}
-
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = avcharHeight;
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += avcharHeight;
}
- int cHeight = alheight * av.charHeight
- + hgap
- + annotationHeight;
+ int cHeight = alheight * avcharHeight + hgap + annotationHeight;
int rowSize = av.getEndRes() - av.getStartRes();
-
// Draw the rest of the panels
- for (int ypos = hgap, row = av.startRes;
- (ypos <= getSize().height) && (row < maxwidth);
- ypos += cHeight, row += rowSize)
+ for (int ypos = hgap, row = av.startRes; (ypos <= getSize().height)
+ && (row < maxwidth); ypos += cHeight, row += rowSize)
{
for (int i = starty; i < alheight; i++)
{
- SequenceI s = av.alignment.getSequenceAt(i);
+ SequenceI s = av.getAlignment().getSequenceAt(i);
gg.setFont(italic);
- if (av.hasHiddenRows)
+ if (doHiddenCheck)
{
setHiddenFont(s);
}
- drawIdString(gg, s, i, 0, ypos);
+ drawIdString(gg, hiddenRows, s, i, 0, ypos);
}
if (labels != null)
{
- gg.translate(0, ypos + (alheight * av.charHeight));
+ gg.translate(0, ypos + (alheight * avcharHeight));
labels.drawComponent(gg, getSize().width);
- gg.translate(0, -ypos - (alheight * av.charHeight));
+ gg.translate(0, -ypos - (alheight * avcharHeight));
}
}
}
else
{
- //Now draw the id strings
+ // Now draw the id strings
SequenceI seq;
for (int i = starty; i < endy; i++)
{
- seq = av.alignment.getSequenceAt(i);
+ seq = av.getAlignment().getSequenceAt(i);
if (seq == null)
{
continue;
}
gg.setFont(italic);
- //boolean isrep=false;
- if (av.hasHiddenRows)
+ // boolean isrep=false;
+ if (doHiddenCheck)
{
- //isrep =
+ // isrep =
setHiddenFont(seq);
}
// Selected sequence colours
- if ( (searchResults != null) &&
- searchResults.contains(seq))
+ if ((searchResults != null) && searchResults.contains(seq))
{
currentColor = Color.black;
currentTextColor = Color.white;
}
- else if ( (av.getSelectionGroup() != null) &&
- av.getSelectionGroup().getSequences(null).contains(seq))
+ else if ((av.getSelectionGroup() != null)
+ && av.getSelectionGroup().getSequences(null).contains(seq))
{
currentColor = Color.lightGray;
currentTextColor = Color.black;
@@ -279,17 +296,17 @@ public class IdCanvas
}
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);
+ // 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);
- gg.drawString(seq.getDisplayId(av.getShowJVSuffix()),
- 0,
- ( ( (i - starty) * av.charHeight) + av.charHeight) -
- (av.charHeight / 5));
+ gg.drawString(seq.getDisplayId(av.getShowJVSuffix()), 0,
+ (((i - starty) * avcharHeight) + avcharHeight)
+ - (avcharHeight / 5));
- if (av.hasHiddenRows && av.showHiddenMarkers)
+ if (hiddenRows)
{
drawMarker(i, starty, 0);
}
@@ -297,24 +314,23 @@ public class IdCanvas
}
}
- public void setHighlighted(java.util.Vector found)
+ public void setHighlighted(List 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)
@@ -340,41 +356,29 @@ public class IdCanvas
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.isHiddenRepSequence(seq))
{
gg.setFont(bold);
return true;