X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdCanvas.java;h=7ce4778a09caeb16090aa71e448a1363739a112e;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=38a13103dc7e4aa21c8966544c13f9c595270671;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/appletgui/IdCanvas.java b/src/jalview/appletgui/IdCanvas.java
index 38a1310..7ce4778 100755
--- a/src/jalview/appletgui/IdCanvas.java
+++ b/src/jalview/appletgui/IdCanvas.java
@@ -1,23 +1,27 @@
/*
- * 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 2.8.2b1)
+ * Copyright (C) 2014 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 java.util.List;
import jalview.datamodel.*;
@@ -39,7 +43,7 @@ public class IdCanvas extends Panel
boolean fastPaint = false;
- java.util.Vector searchResults;
+ List searchResults;
public IdCanvas(AlignViewport av)
{
@@ -80,7 +84,7 @@ public class IdCanvas extends Panel
((i - starty) * charHeight) + ypos + charHeight
- (charHeight / 5));
- if (av.hasHiddenRows && av.showHiddenMarkers)
+ if (av.hasHiddenRows() && av.showHiddenMarkers)
{
drawMarker(i, starty, ypos);
}
@@ -186,10 +190,10 @@ public class IdCanvas extends Panel
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;
}
@@ -221,9 +225,9 @@ public class IdCanvas extends Panel
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 (av.hasHiddenRows())
{
setHiddenFont(s);
}
@@ -246,14 +250,14 @@ public class IdCanvas extends Panel
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)
+ if (av.hasHiddenRows())
{
// isrep =
setHiddenFont(seq);
@@ -288,7 +292,7 @@ public class IdCanvas extends Panel
(((i - starty) * av.charHeight) + av.charHeight)
- (av.charHeight / 5));
- if (av.hasHiddenRows && av.showHiddenMarkers)
+ if (av.hasHiddenRows() && av.showHiddenMarkers)
{
drawMarker(i, starty, 0);
}
@@ -296,15 +300,15 @@ public class IdCanvas extends Panel
}
}
- 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;
+ SequenceI[] hseqs = av.getAlignment().getHiddenSequences().hiddenSequences;
// Use this method here instead of calling hiddenSeq adjust
// 3 times.
int hSize = hseqs.length;
@@ -362,8 +366,8 @@ public class IdCanvas extends Panel
Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont()
.getSize());
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(seq))
+ if (av.getHiddenRepSequences() != null
+ && av.getHiddenRepSequences().containsKey(seq))
{
gg.setFont(bold);
return true;