/*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * 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 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.
+ *
+ * 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.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
-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
{
for (int i = scalestartx; i < endx; i += 10)
{
int value = i;
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
value = av.getColumnSelection().adjustForHiddenColumns(value);
}
{
FontMetrics fm = getFontMetrics(av.getFont());
ypos += av.charHeight;
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
startx = av.getColumnSelection().adjustForHiddenColumns(startx);
endx = av.getColumnSelection().adjustForHiddenColumns(endx);
}
- int maxwidth = av.alignment.getWidth();
- if (av.hasHiddenColumns)
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
// 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;
continue;
}
- value = av.alignment.getSequenceAt(i).findPosition(index);
+ value = av.getAlignment().getSequenceAt(i).findPosition(index);
break;
}
{
ypos += av.charHeight;
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
endx = av.getColumnSelection().adjustForHiddenColumns(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;
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;
int endx;
int ypos = hgap;
- int maxwidth = av.alignment.getWidth() - 1;
+ int maxwidth = av.getAlignment().getWidth() - 1;
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
{
drawNorthScale(g, startRes, endx, ypos);
}
- if (av.hasHiddenColumns && av.showHiddenMarkers)
+ if (av.hasHiddenColumns() && av.showHiddenMarkers)
{
g.setColor(Color.blue);
int res;
void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
int endSeq, 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;
- 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];
+
+ if (hideStart <= blockStart)
+ {
+ blockStart += (hideEnd - hideStart) + 1;
+ continue;
+ }
- blockEnd = hideStart - 1;
+ blockEnd = hideStart - 1;
- g1.translate(screenY * av.charWidth, 0);
+ g1.translate(screenY * av.charWidth, 0);
- draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
+ draw(g1, blockStart, blockEnd, startSeq, endSeq, offset);
- 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);
- }
+ 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);
+ }
- g1.translate(-screenY * av.charWidth, 0);
- screenY += blockEnd - blockStart + 1;
- blockStart = hideEnd + 1;
+ g1.translate(-screenY * av.charWidth, 0);
+ screenY += blockEnd - blockStart + 1;
+ blockStart = hideEnd + 1;
+ }
}
-
if (screenY <= (endRes - startRes))
{
blockEnd = blockStart + (endRes - startRes) - screenY;
// ///////////////////////////
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),
+ sr.drawSequence(nextSeq, av.getAlignment().findAllGroups(nextSeq),
startRes, endRes, offset + ((i - startSeq) * av.charHeight));
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
fr.drawSequence(g, nextSeq, startRes, endRes, offset
+ ((i - startSeq) * av.charHeight));
}
if (av.getSelectionGroup() != null
- || av.alignment.getGroups().size() > 0)
+ || av.getAlignment().getGroups().size() > 0)
{
drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
}
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;
}
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++)
{
if ((sx <= (endRes - startRes) * av.charWidth)
&& group.getSequences(null).contains(
- av.alignment.getSequenceAt(i)))
+ av.getAlignment().getSequenceAt(i)))
{
if ((bottom == -1)
&& (i >= alHeight || !group.getSequences(null)
- .contains(av.alignment.getSequenceAt(i + 1))))
+ .contains(
+ av.getAlignment().getSequenceAt(i + 1))))
{
bottom = sy + av.charHeight;
}
{
if (((top == -1) && (i == 0))
|| !group.getSequences(null).contains(
- av.alignment.getSequenceAt(i - 1)))
+ av.getAlignment().getSequenceAt(i - 1)))
{
top = sy;
}
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());
}
}
git://source.jalview.org / jalview.git / blobdiff