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JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob
[jalview.git]
/
src
/
jalview
/
gui
/
AlignmentPanel.java
diff --git
a/src/jalview/gui/AlignmentPanel.java
b/src/jalview/gui/AlignmentPanel.java
index
ad7e75c
..
1906829
100644
(file)
--- a/
src/jalview/gui/AlignmentPanel.java
+++ b/
src/jalview/gui/AlignmentPanel.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-76,6
+76,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
private IdPanel idPanel;
private boolean headless;
private IdPanel idPanel;
private boolean headless;
+
IdwidthAdjuster idwidthAdjuster;
/** DOCUMENT ME!! */
IdwidthAdjuster idwidthAdjuster;
/** DOCUMENT ME!! */
@@
-155,6
+156,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
{
return av;
}
{
return av;
}
+
public void alignmentChanged()
{
av.alignmentChanged(this);
public void alignmentChanged()
{
av.alignmentChanged(this);
@@
-177,8
+179,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
+ fm.getDescent()));
idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
+ fm.getDescent()));
idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
- .getCharHeight()
- + fm.getDescent()));
+ .getCharHeight() + fm.getDescent()));
getIdPanel().getIdCanvas().gg = null;
getSeqPanel().seqCanvas.img = null;
getIdPanel().getIdCanvas().gg = null;
getSeqPanel().seqCanvas.img = null;
@@
-317,7
+318,8
@@
public class AlignmentPanel extends GAlignmentPanel implements
* @param redrawOverview
* @return
*/
* @param redrawOverview
* @return
*/
- public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview)
+ public boolean scrollToPosition(SearchResults searchResults,
+ boolean redrawOverview)
{
return scrollToPosition(searchResults, 0, redrawOverview, false);
}
{
return scrollToPosition(searchResults, 0, redrawOverview, false);
}
@@
-337,8
+339,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
* @return false if results were not found
*/
public boolean scrollToPosition(SearchResults results,
* @return false if results were not found
*/
public boolean scrollToPosition(SearchResults results,
- int verticalOffset,
- boolean redrawOverview, boolean centre)
+ int verticalOffset, boolean redrawOverview, boolean centre)
{
int startv, endv, starts, ends;
// TODO: properly locate search results in view when large numbers of hidden
{
int startv, endv, starts, ends;
// TODO: properly locate search results in view when large numbers of hidden
@@
-362,8
+363,9
@@
public class AlignmentPanel extends GAlignmentPanel implements
}
int start = r[0];
int end = r[1];
}
int start = r[0];
int end = r[1];
- // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
// DEBUG
// DEBUG
+ // System.err.println(this.av.viewName + " Seq : " + seqIndex
+ // + " Scroll to " + start + "," + end);
/*
* To centre results, scroll to positions half the visible width
/*
* To centre results, scroll to positions half the visible width
@@
-373,7
+375,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
{
int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
start = Math.max(start - offset, 0);
{
int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
start = Math.max(start - offset, 0);
- end = Math.min(end + offset, seq.getEnd() - 1);
+ end = end + offset - 1;
}
if (start < 0)
{
}
if (start < 0)
{
@@
-402,6
+404,9
@@
public class AlignmentPanel extends GAlignmentPanel implements
*/
seqIndex = Math.max(0, seqIndex - verticalOffset);
*/
seqIndex = Math.max(0, seqIndex - verticalOffset);
+ // System.out.println("start=" + start + ", end=" + end + ", startv="
+ // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
+ // + av.getStartSeq() + ", ends=" + av.getEndSeq());
if (!av.getWrapAlignment())
{
if ((startv = av.getStartRes()) >= start)
if (!av.getWrapAlignment())
{
if ((startv = av.getStartRes()) >= start)
@@
-668,14
+673,14
@@
public class AlignmentPanel extends GAlignmentPanel implements
* Adjust row/column scrollers to show a visible position in the alignment.
*
* @param x
* Adjust row/column scrollers to show a visible position in the alignment.
*
* @param x
- * visible column to scroll to DOCUMENT ME!
+ * visible column to scroll to
* @param y
* visible row to scroll to
*
*/
public void setScrollValues(int x, int y)
{
* @param y
* visible row to scroll to
*
*/
public void setScrollValues(int x, int y)
{
- // System.err.println("Scroll to "+x+","+y);
+ // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
if (av == null || av.getAlignment() == null)
{
return;
if (av == null || av.getAlignment() == null)
{
return;
@@
-743,7
+748,8
@@
public class AlignmentPanel extends GAlignmentPanel implements
{
int x = hscroll.getValue();
av.setStartRes(x);
{
int x = hscroll.getValue();
av.setStartRes(x);
- av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1);
+ av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+ .getCharWidth())) - 1);
}
if (evt.getSource() == vscroll)
}
if (evt.getSource() == vscroll)
@@
-840,13
+846,13
@@
public class AlignmentPanel extends GAlignmentPanel implements
{
final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
av.isShowAutocalculatedAbove());
{
final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
av.isShowAutocalculatedAbove());
- sorter.sort(getAlignment()
- .getAlignmentAnnotation(),
+ sorter.sort(getAlignment().getAlignmentAnnotation(),
av.getSortAnnotationsBy());
repaint();
if (updateOverview)
{
av.getSortAnnotationsBy());
repaint();
if (updateOverview)
{
+ // TODO: determine if this paintAlignment changed structure colours
av.getStructureSelectionManager().sequenceColoursChanged(this);
if (overviewPanel != null)
av.getStructureSelectionManager().sequenceColoursChanged(this);
if (overviewPanel != null)
@@
-1058,9
+1064,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
- 4;
}
- 4;
}
- pg.drawString(
- seq.getDisplayId(av.getShowJVSuffix()),
- xPos,
+ pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
(((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
- (av.getCharHeight() / 5));
}
(((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
- (av.getCharHeight() / 5));
}
@@
-1069,7
+1073,8
@@
public class AlignmentPanel extends GAlignmentPanel implements
// draw main sequence panel
pg.translate(idWidth, 0);
// draw main sequence panel
pg.translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
+ getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq,
+ endSeq, 0);
if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
{
if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
{
@@
-1171,12
+1176,14
@@
public class AlignmentPanel extends GAlignmentPanel implements
}
if (labels != null)
{
}
if (labels != null)
{
- pg.translate(-3, ypos
- + (av.getAlignment().getHeight() * av.getCharHeight()));
+ pg.translate(-3,
+ ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
pg.setFont(av.getFont());
labels.drawComponent(pg, idWidth);
pg.setFont(av.getFont());
labels.drawComponent(pg, idWidth);
- pg.translate(+3, -ypos
+ pg.translate(
+ +3,
+ -ypos
- (av.getAlignment().getHeight() * av
.getCharHeight()));
}
- (av.getAlignment().getHeight() * av
.getCharHeight()));
}
@@
-1186,8
+1193,8
@@
public class AlignmentPanel extends GAlignmentPanel implements
pg.translate(idWidth, 0);
pg.translate(idWidth, 0);
- getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
- 0);
+ getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+ totalHeight, 0);
if ((pi * pheight) < totalHeight)
{
if ((pi * pheight) < totalHeight)
{
@@
-1245,8
+1252,8
@@
public class AlignmentPanel extends GAlignmentPanel implements
if (alignFrame != null && !headless)
{
alignFrame.setProgressBar(MessageManager.formatMessage(
if (alignFrame != null && !headless)
{
alignFrame.setProgressBar(MessageManager.formatMessage(
- "status.saving_file", new Object[]
- { type.getLabel() }), progress);
+ "status.saving_file", new Object[] { type.getLabel() }),
+ progress);
}
try
{
}
try
{
@@
-1307,7
+1314,9
@@
public class AlignmentPanel extends GAlignmentPanel implements
{
if (alignFrame != null && !headless)
{
{
if (alignFrame != null && !headless)
{
- alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress);
+ alignFrame.setProgressBar(
+ MessageManager.getString("status.export_complete"),
+ progress);
}
}
}
}
}
}
@@
-1372,6
+1381,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
{
makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
}
{
makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
}
+
public void makePNGImageMap(File imgMapFile, String imageName)
{
// /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
public void makePNGImageMap(File imgMapFile, String imageName)
{
// /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
@@
-1409,8
+1419,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
if (av.getAlignment().isNucleotide())
{
triplet = ResidueProperties.nucleotideName.get(seq
if (av.getAlignment().isNucleotide())
{
triplet = ResidueProperties.nucleotideName.get(seq
- .getCharAt(res)
- + "");
+ .getCharAt(res) + "");
}
else
{
}
else
{
@@
-1432,8
+1441,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
text.append("<area shape=\"rect\" coords=\""
+ (idWidth + res * av.getCharWidth()) + "," + sy
+ "," + (idWidth + (res + 1) * av.getCharWidth())
text.append("<area shape=\"rect\" coords=\""
+ (idWidth + res * av.getCharWidth()) + "," + sy
+ "," + (idWidth + (res + 1) * av.getCharWidth())
- + ","
- + (av.getCharHeight() + sy) + "\""
+ + "," + (av.getCharHeight() + sy) + "\""
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
@@
-1452,8
+1460,7
@@
public class AlignmentPanel extends GAlignmentPanel implements
text.append("<area shape=\"rect\" coords=\""
+ (idWidth + res * av.getCharWidth()) + "," + sy
+ "," + (idWidth + (res + 1) * av.getCharWidth())
text.append("<area shape=\"rect\" coords=\""
+ (idWidth + res * av.getCharWidth()) + "," + sy
+ "," + (idWidth + (res + 1) * av.getCharWidth())
- + ","
- + (av.getCharHeight() + sy) + "\""
+ + "," + (av.getCharHeight() + sy) + "\""
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
+ " onMouseOver=\"toolTip('" + alIndex + " "
+ triplet);
}
@@
-1609,10
+1616,9
@@
public class AlignmentPanel extends GAlignmentPanel implements
@Override
public AlignmentI getAlignment()
{
@Override
public AlignmentI getAlignment()
{
- return av.getAlignment();
+ return av == null ? null : av.getAlignment();
}
}
-
@Override
public String getViewName()
{
@Override
public String getViewName()
{
@@
-1664,12
+1670,15
@@
public class AlignmentPanel extends GAlignmentPanel implements
return new FeatureRenderer(this);
}
return new FeatureRenderer(this);
}
- @Override
+
+ @Override
public jalview.api.FeatureRenderer getFeatureRenderer()
{
return seqPanel.seqCanvas.getFeatureRenderer();
}
public jalview.api.FeatureRenderer getFeatureRenderer()
{
return seqPanel.seqCanvas.getFeatureRenderer();
}
- public void updateFeatureRenderer(jalview.renderer.seqfeatures.FeatureRenderer fr)
+
+ public void updateFeatureRenderer(
+ jalview.renderer.seqfeatures.FeatureRenderer fr)
{
fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
}
{
fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
}