X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FOverviewPanel.java;h=8486fe0bc4681494df18f3a3425f0c1177110074;hb=7a2f4e9ee4119f0369743e7996bcebbb6ab46f9e;hp=4b646c3ab9832af2569145c36f958e48e0615e50;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git
diff --git a/src/jalview/appletgui/OverviewPanel.java b/src/jalview/appletgui/OverviewPanel.java
index 4b646c3..8486fe0 100755
--- a/src/jalview/appletgui/OverviewPanel.java
+++ b/src/jalview/appletgui/OverviewPanel.java
@@ -1,19 +1,22 @@
/*
- * 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 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;
@@ -66,8 +69,7 @@ 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.getAlignment().getWidth()
/ (float) av.getAlignment().getHeight();
@@ -102,6 +104,7 @@ public class OverviewPanel extends Panel implements Runnable,
addComponentListener(new ComponentAdapter()
{
+ @Override
public void componentResized(ComponentEvent evt)
{
if (getSize().width != width
@@ -120,22 +123,27 @@ 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();
@@ -143,6 +151,7 @@ public class OverviewPanel extends Panel implements Runnable,
checkValid();
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
boxX = evt.getX();
@@ -150,6 +159,7 @@ public class OverviewPanel extends Panel implements Runnable,
checkValid();
}
+ @Override
public void mouseDragged(MouseEvent evt)
{
boxX = evt.getX();
@@ -199,8 +209,8 @@ public class OverviewPanel extends Panel implements Runnable,
if (av.hasHiddenRows())
{
- row = av.getAlignment().getHiddenSequences().findIndexWithoutHiddenSeqs(
- row);
+ row = av.getAlignment().getHiddenSequences()
+ .findIndexWithoutHiddenSeqs(row);
}
ap.setScrollValues(col, row);
@@ -218,10 +228,9 @@ 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;
@@ -242,13 +251,14 @@ public class OverviewPanel extends Panel implements Runnable,
// the overview is being calculated
boolean resizeAgain = false;
+ @Override
public void run()
{
miniMe = null;
int alwidth = av.getAlignment().getWidth();
int alheight = av.getAlignment().getHeight();
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
fr.transferSettings(ap.seqPanel.seqCanvas.getFeatureRenderer());
}
@@ -280,7 +290,7 @@ public class OverviewPanel extends Panel implements Runnable,
int row, col, sameRow = 0, sameCol = 0;
jalview.datamodel.SequenceI seq;
boolean hiddenRow = false;
- AlignmentI alignment=av.getAlignment();
+ AlignmentI alignment = av.getAlignment();
for (row = 0; row <= sequencesHeight; row++)
{
if ((int) (row * sampleRow) == lastrow)
@@ -325,7 +335,7 @@ public class OverviewPanel extends Panel implements Runnable,
{
color = sr.getResidueBoxColour(seq, lastcol);
- if (av.showSequenceFeatures)
+ if (av.isShowSequenceFeatures())
{
color = fr.findFeatureColour(color, seq, lastcol);
}
@@ -360,14 +370,16 @@ public class OverviewPanel extends Panel implements Runnable,
sameRow = 1;
}
- if (av.getAlignmentConservationAnnotation()!= 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.getAlignmentConservationAnnotation(),
+ 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);
@@ -391,7 +403,8 @@ public class OverviewPanel extends Panel implements Runnable,
{
int fullsizeWidth = av.getAlignment().getWidth() * av.getCharWidth();
int fullsizeHeight = (av.getAlignment().getHeight() + av.getAlignment()
- .getHiddenSequences().getSize()) * av.getCharHeight();
+ .getHiddenSequences().getSize())
+ * av.getCharHeight();
int startRes = av.getStartRes();
int endRes = av.getEndRes();
@@ -407,8 +420,8 @@ public class OverviewPanel extends Panel implements Runnable,
if (av.hasHiddenRows())
{
- startSeq = av.getAlignment().getHiddenSequences().adjustForHiddenSeqs(
- startSeq);
+ startSeq = av.getAlignment().getHiddenSequences()
+ .adjustForHiddenSeqs(startSeq);
endSeq = av.getAlignment().getHiddenSequences()
.adjustForHiddenSeqs(endSeq);
@@ -435,11 +448,13 @@ 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();