X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=5c5ae84302a14b49cce29bf4e2f8b8312bb9b832;hb=a4677746324adeea9632d7306c83dfd94dff6181;hp=fc4fb8c813d72187ac983dc1cd3446abb3f677f9;hpb=298c2b85845dbaabda7e3304751cc856e7b0ad30;p=jalview.git
diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index fc4fb8c..5c5ae84 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -1,24 +1,39 @@
/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.awt.event.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
public class OverviewPanel extends Panel implements Runnable,
MouseMotionListener, MouseListener
@@ -64,18 +79,17 @@ public class OverviewPanel extends Panel implements Runnable,
sr.renderGaps = false;
sr.forOverview = true;
fr = new FeatureRenderer(av);
- fr.overview = true;
// scale the initial size of overviewpanel to shape of alignment
- float initialScale = (float) av.alignment.getWidth()
- / (float) av.alignment.getHeight();
+ float initialScale = (float) av.getAlignment().getWidth()
+ / (float) av.getAlignment().getHeight();
- if (av.hconsensus == null)
+ if (av.getSequenceConsensusHash() == null)
{
graphHeight = 0;
}
- if (av.alignment.getWidth() > av.alignment.getHeight())
+ if (av.getAlignment().getWidth() > av.getAlignment().getHeight())
{
// wider
width = 400;
@@ -100,6 +114,7 @@ public class OverviewPanel extends Panel implements Runnable,
addComponentListener(new ComponentAdapter()
{
+ @Override
public void componentResized(ComponentEvent evt)
{
if (getSize().width != width
@@ -118,22 +133,27 @@ public class OverviewPanel extends Panel implements Runnable,
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
}
+ @Override
public void mouseExited(MouseEvent evt)
{
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mouseMoved(MouseEvent evt)
{
}
+ @Override
public void mousePressed(MouseEvent evt)
{
boxX = evt.getX();
@@ -141,6 +161,7 @@ public class OverviewPanel extends Panel implements Runnable,
checkValid();
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
boxX = evt.getX();
@@ -148,6 +169,7 @@ public class OverviewPanel extends Panel implements Runnable,
checkValid();
}
+ @Override
public void mouseDragged(MouseEvent evt)
{
boxX = evt.getX();
@@ -174,7 +196,7 @@ public class OverviewPanel extends Panel implements Runnable,
if (boxX > (width - boxWidth))
{
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
// Try smallest possible box
boxWidth = (int) ((av.endRes - av.startRes + 1) * av.getCharWidth() * scalew);
@@ -185,7 +207,7 @@ public class OverviewPanel extends Panel implements Runnable,
int col = (int) (boxX / scalew / av.getCharWidth());
int row = (int) (boxY / scaleh / av.getCharHeight());
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
if (!av.getColumnSelection().isVisible(col))
{
@@ -195,10 +217,10 @@ public class OverviewPanel extends Panel implements Runnable,
col = av.getColumnSelection().findColumnPosition(col);
}
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
- row = av.alignment.getHiddenSequences().findIndexWithoutHiddenSeqs(
- row);
+ row = av.getAlignment().getHiddenSequences()
+ .findIndexWithoutHiddenSeqs(row);
}
ap.setScrollValues(col, row);
@@ -216,10 +238,9 @@ public class OverviewPanel extends Panel implements Runnable,
return;
}
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
- fr.featureGroups = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups;
- fr.featureColours = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours;
+ fr.transferSettings(ap.seqPanel.seqCanvas.fr);
}
resizing = true;
@@ -240,13 +261,14 @@ public class OverviewPanel extends Panel implements Runnable,
// the overview is being calculated
boolean resizeAgain = false;
+ @Override
public void run()
{
miniMe = null;
- int alwidth = av.alignment.getWidth();
- int alheight = av.alignment.getHeight();
+ int alwidth = av.getAlignment().getWidth();
+ int alheight = av.getAlignment().getHeight();
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
}
@@ -276,8 +298,11 @@ public class OverviewPanel extends Panel implements Runnable,
int xstart = 0, ystart = 0;
Color color = Color.yellow;
int row, col, sameRow = 0, sameCol = 0;
- jalview.datamodel.SequenceI seq;
+ SequenceI seq;
+ final boolean hasHiddenRows = av.hasHiddenRows(), hasHiddenCols = av
+ .hasHiddenColumns();
boolean hiddenRow = false;
+ AlignmentI alignment = av.getAlignment();
for (row = 0; row <= sequencesHeight; row++)
{
if ((int) (row * sampleRow) == lastrow)
@@ -287,15 +312,15 @@ public class OverviewPanel extends Panel implements Runnable,
}
hiddenRow = false;
- if (av.hasHiddenRows)
+ if (hasHiddenRows)
{
- seq = av.alignment.getHiddenSequences().getHiddenSequence(lastrow);
+ seq = alignment.getHiddenSequences().getHiddenSequence(lastrow);
if (seq == null)
{
- int index = av.alignment.getHiddenSequences()
+ int index = alignment.getHiddenSequences()
.findIndexWithoutHiddenSeqs(lastrow);
- seq = av.alignment.getSequenceAt(index);
+ seq = alignment.getSequenceAt(index);
}
else
{
@@ -304,7 +329,7 @@ public class OverviewPanel extends Panel implements Runnable,
}
else
{
- seq = av.alignment.getSequenceAt(lastrow);
+ seq = alignment.getSequenceAt(lastrow);
}
for (col = 0; col < width; col++)
@@ -322,7 +347,7 @@ public class OverviewPanel extends Panel implements Runnable,
{
color = sr.getResidueBoxColour(seq, lastcol);
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
color = fr.findFeatureColour(color, seq, lastcol);
}
@@ -333,7 +358,7 @@ public class OverviewPanel extends Panel implements Runnable,
}
if (hiddenRow
- || (av.hasHiddenColumns && !av.getColumnSelection()
+ || (hasHiddenCols && !av.getColumnSelection()
.isVisible(lastcol)))
{
color = color.darker().darker();
@@ -357,14 +382,16 @@ public class OverviewPanel extends Panel implements Runnable,
sameRow = 1;
}
- if (av.conservation != null)
+ if (av.getAlignmentConservationAnnotation() != null)
{
for (col = 0; col < width; col++)
{
lastcol = (int) (col * sampleCol);
{
mg.translate(col, sequencesHeight);
- ap.annotationPanel.renderer.drawGraph(mg, av.conservation,
+ ap.annotationPanel.renderer.drawGraph(mg,
+ av.getAlignmentConservationAnnotation(),
+ av.getAlignmentConservationAnnotation().annotations,
(int) (sampleCol) + 1, graphHeight,
(int) (col * sampleCol), (int) (col * sampleCol) + 1);
mg.translate(-col, -sequencesHeight);
@@ -386,14 +413,15 @@ public class OverviewPanel extends Panel implements Runnable,
public void setBoxPosition()
{
- int fullsizeWidth = av.alignment.getWidth() * av.getCharWidth();
- int fullsizeHeight = (av.alignment.getHeight() + av.alignment
- .getHiddenSequences().getSize()) * av.getCharHeight();
+ int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
+ int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
+ .getHiddenSequences().getSize())
+ * av.getCharHeight();
int startRes = av.getStartRes();
int endRes = av.getEndRes();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
startRes = av.getColumnSelection().adjustForHiddenColumns(startRes);
endRes = av.getColumnSelection().adjustForHiddenColumns(endRes);
@@ -402,12 +430,12 @@ public class OverviewPanel extends Panel implements Runnable,
int startSeq = av.startSeq;
int endSeq = av.endSeq;
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
- startSeq = av.alignment.getHiddenSequences().adjustForHiddenSeqs(
- startSeq);
+ startSeq = av.getAlignment().getHiddenSequences()
+ .adjustForHiddenSeqs(startSeq);
- endSeq = av.alignment.getHiddenSequences()
+ endSeq = av.getAlignment().getHiddenSequences()
.adjustForHiddenSeqs(endSeq);
}
@@ -418,7 +446,7 @@ public class OverviewPanel extends Panel implements Runnable,
boxX = (int) (startRes * av.getCharWidth() * scalew);
boxY = (int) (startSeq * av.getCharHeight() * scaleh);
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
boxWidth = (int) ((endRes - startRes + 1) * av.getCharWidth() * scalew);
}
@@ -432,11 +460,13 @@ public class OverviewPanel extends Panel implements Runnable,
repaint();
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
Graphics og = offscreen.getGraphics();