X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqCanvas.java;h=9c2fd7393c8c10d37107a1acbccd10f0f0802e88;hb=10ff37d2cb03f342ddbed679951d3e2fef0a404b;hp=26da08b779f0f60d1fac3a3cb29566687a3ff8b8;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 26da08b..9c2fd73 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, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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 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;
+import java.util.List;
public class SeqCanvas extends Panel
{
@@ -78,7 +89,7 @@ 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);
}
@@ -97,22 +108,22 @@ public class SeqCanvas extends Panel
{
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;
@@ -125,7 +136,7 @@ public class SeqCanvas extends Panel
continue;
}
- value = av.alignment.getSequenceAt(i).findPosition(index);
+ value = av.getAlignment().getSequenceAt(i).findPosition(index);
break;
}
@@ -144,16 +155,16 @@ public class SeqCanvas extends Panel
{
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;
@@ -348,9 +359,10 @@ 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;
@@ -397,9 +409,9 @@ public class SeqCanvas extends Panel
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;
}
@@ -433,7 +445,7 @@ public class SeqCanvas extends Panel
{
drawNorthScale(g, startRes, endx, ypos);
}
- if (av.hasHiddenColumns && av.showHiddenMarkers)
+ if (av.hasHiddenColumns() && av.showHiddenMarkers)
{
g.setColor(Color.blue);
int res;
@@ -506,21 +518,20 @@ public class SeqCanvas extends Panel
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();
+ List regions = av.getColumnSelection().getHiddenColumns();
int screenY = 0;
int blockStart = startRes;
int blockEnd = endRes;
- for (int i = 0; i < regions.size(); i++)
+ for (int[] region : regions)
{
- int[] region = (int[]) regions.elementAt(i);
int hideStart = region[0];
int hideEnd = region[1];
@@ -575,14 +586,14 @@ public class SeqCanvas extends Panel
// ///////////////////////////
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)
@@ -619,7 +630,7 @@ public class SeqCanvas extends Panel
}
if (av.getSelectionGroup() != null
- || av.alignment.getGroups().size() > 0)
+ || av.getAlignment().getGroups().size() > 0)
{
drawGroupsBoundaries(g, startRes, endRes, startSeq, endSeq, offset);
}
@@ -640,9 +651,9 @@ 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;
}
@@ -655,7 +666,7 @@ 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++)
{
@@ -670,11 +681,12 @@ public class SeqCanvas extends Panel
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;
}
@@ -683,7 +695,7 @@ public class SeqCanvas extends Panel
{
if (((top == -1) && (i == 0))
|| !group.getSequences(null).contains(
- av.alignment.getSequenceAt(i - 1)))
+ av.getAlignment().getSequenceAt(i - 1)))
{
top = sy;
}
@@ -793,14 +805,14 @@ 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());
}
}