X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignmentPanel.java;h=3ae0394f4ce9c62d72a28509013407363c101e41;hb=97b26ba418dec7a6e926378205d25470bf098633;hp=4941b1154f0d067126b3f6062d4cd780c262c7b0;hpb=ad20cd92225f2ee8c251d39b00b90555d382a616;p=jalview.git
diff --git a/src/jalview/appletgui/AlignmentPanel.java b/src/jalview/appletgui/AlignmentPanel.java
index 4941b11..3ae0394 100644
--- a/src/jalview/appletgui/AlignmentPanel.java
+++ b/src/jalview/appletgui/AlignmentPanel.java
@@ -1,28 +1,48 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.*;
+import jalview.bin.JalviewLite;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceI;
import jalview.structure.StructureSelectionManager;
+import jalview.viewmodel.ViewportRanges;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.FontMetrics;
+import java.awt.Frame;
+import java.awt.Graphics;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.util.List;
public class AlignmentPanel extends Panel implements AdjustmentListener,
AlignmentViewPanel
@@ -46,13 +66,17 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
AnnotationLabels alabels;
+ ViewportRanges vpRanges;
+
// this value is set false when selection area being dragged
boolean fastPaint = true;
- public void finalize()
+ @Override
+ public void finalize() throws Throwable
{
alignFrame = null;
av = null;
+ vpRanges = null;
seqPanel = null;
seqPanelHolder = null;
sequenceHolderPanel = null;
@@ -61,6 +85,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
annotationPanel = null;
annotationPanelHolder = null;
annotationSpaceFillerHolder = null;
+ super.finalize();
}
public AlignmentPanel(AlignFrame af, final AlignViewport av)
@@ -75,6 +100,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
alignFrame = af;
this.av = av;
+ vpRanges = av.getRanges();
seqPanel = new SeqPanel(av, this);
idPanel = new IdPanel(av, this);
scalePanel = new ScalePanel(av, this);
@@ -83,10 +109,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
annotationPanelHolder.add(annotationPanel, BorderLayout.CENTER);
sequenceHolderPanel.add(annotationPanelHolder, BorderLayout.SOUTH);
-
alabels = new AnnotationLabels(this);
- setAnnotationVisible(av.showAnnotation);
+ setAnnotationVisible(av.isShowAnnotation());
idPanelHolder.add(idPanel, BorderLayout.CENTER);
idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
@@ -103,9 +128,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
addComponentListener(new ComponentAdapter()
{
+ @Override
public void componentResized(ComponentEvent evt)
{
- setScrollValues(av.getStartRes(), av.getStartSeq());
+ setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
if (getSize().height > 0
&& annotationPanelHolder.getSize().height > 0)
{
@@ -128,6 +154,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
final AlignmentPanel ap = this;
av.addPropertyChangeListener(new java.beans.PropertyChangeListener()
{
+ @Override
public void propertyChange(java.beans.PropertyChangeEvent evt)
{
if (evt.getPropertyName().equals("alignment"))
@@ -137,7 +164,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
}
}
});
+ }
+ @Override
+ public AlignViewportI getAlignViewport()
+ {
+ return av;
}
public SequenceRenderer getSequenceRenderer()
@@ -145,11 +177,20 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
return seqPanel.seqCanvas.sr;
}
- public FeatureRenderer getFeatureRenderer()
+ @Override
+ public jalview.api.FeatureRenderer getFeatureRenderer()
{
return seqPanel.seqCanvas.fr;
}
+ @Override
+ public jalview.api.FeatureRenderer cloneFeatureRenderer()
+ {
+ FeatureRenderer nfr = new FeatureRenderer(av);
+ nfr.transferSettings(seqPanel.seqCanvas.fr);
+ return nfr;
+ }
+
public void alignmentChanged()
{
av.alignmentChanged(this);
@@ -171,8 +212,9 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
idPanel.idCanvas.image = null;
FontMetrics fm = getFontMetrics(av.getFont());
- scalePanel.setSize(new Dimension(10, av.charHeight + fm.getDescent()));
- idwidthAdjuster.setSize(new Dimension(10, av.charHeight
+ scalePanel.setSize(new Dimension(10, av.getCharHeight()
+ + fm.getDescent()));
+ idwidthAdjuster.setSize(new Dimension(10, av.getCharHeight()
+ fm.getDescent()));
av.updateSequenceIdColours();
annotationPanel.image = null;
@@ -256,7 +298,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
* Highlight the given results on the alignment.
*
*/
- public void highlightSearchResults(SearchResults results)
+ public void highlightSearchResults(SearchResultsI results)
{
scrollToPosition(results);
seqPanel.seqCanvas.highlightSearchResults(results);
@@ -269,7 +311,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
* @param results
* @return false if results were not found
*/
- public boolean scrollToPosition(SearchResults results)
+ public boolean scrollToPosition(SearchResultsI results)
{
return scrollToPosition(results, true);
}
@@ -283,10 +325,25 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
* - when set, the overview will be recalculated (takes longer)
* @return false if results were not found
*/
- public boolean scrollToPosition(SearchResults results,
+ public boolean scrollToPosition(SearchResultsI results,
boolean redrawOverview)
{
+ return scrollToPosition(results, 0, redrawOverview, false);
+ }
+ /**
+ * scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
+ * @param results
+ * @param redrawOverview
+ * - when set, the overview will be recalculated (takes longer)
+ * @return false if results were not found
+ */
+ public boolean scrollToPosition(SearchResultsI results,
+ int verticalOffset,
+ boolean redrawOverview, boolean centre)
+ {
// do we need to scroll the panel?
if (results != null && results.getSize() > 0)
{
@@ -296,11 +353,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
{
return false;
}
+ /*
+ * allow for offset of target sequence (actually scroll to one above it)
+ */
+
SequenceI seq = alignment.getSequenceAt(seqIndex);
int[] r = results.getResults(seq, 0, alignment.getWidth());
if (r == null)
{
- if (av.applet.debug)
+ if (JalviewLite.debug)
{// DEBUG
System.out
.println("DEBUG: scroll didn't happen - results not within alignment : "
@@ -308,7 +369,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
}
return false;
}
- if (av.applet.debug)
+ if (JalviewLite.debug)
{
// DEBUG
/*
@@ -320,6 +381,18 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
}
int start = r[0];
int end = r[1];
+
+ /*
+ * To centre results, scroll to positions half the visible width
+ * left/right of the start/end positions
+ */
+ if (centre)
+ {
+ int offset = (vpRanges.getEndRes() - vpRanges.getStartRes() + 1) / 2 - 1;
+ start = Math.max(start - offset, 0);
+ end = Math.min(end + offset, seq.getEnd() - 1);
+ }
+
if (start < 0)
{
return false;
@@ -328,6 +401,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
{
return false;
}
+
+ /*
+ * allow for offset of target sequence (actually scroll to one above it)
+ */
+ seqIndex = Math.max(0, seqIndex - verticalOffset);
return scrollTo(start, end, seqIndex, false, redrawOverview);
}
return true;
@@ -356,7 +434,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
{
start = ostart;
}
- if (!av.wrapAlignment)
+
+ if (!av.getWrapAlignment())
{
/*
* int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
@@ -367,33 +446,65 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
* av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
* seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
* setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
- *
- * /*
*/
- if ((av.getStartRes() > end)
- || (av.getEndRes() < start)
- || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
- {
- if (start > av.getAlignment().getWidth() - hextent)
- {
- start = av.getAlignment().getWidth() - hextent;
- if (start < 0)
- {
- start = 0;
- }
- }
- if (seqIndex > av.getAlignment().getHeight() - vextent)
- {
- seqIndex = av.getAlignment().getHeight() - vextent;
- if (seqIndex < 0)
- {
- seqIndex = 0;
- }
- }
- // System.out.println("trying to scroll to: "+start+" "+seqIndex);
- setScrollValues(start, seqIndex);
- }/**/
+ // below is scrolling logic up to Jalview 2.8.2
+ // if ((av.getStartRes() > end)
+ // || (av.getEndRes() < start)
+ // || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+ // {
+ // if (start > av.getAlignment().getWidth() - hextent)
+ // {
+ // start = av.getAlignment().getWidth() - hextent;
+ // if (start < 0)
+ // {
+ // start = 0;
+ // }
+ //
+ // }
+ // if (seqIndex > av.getAlignment().getHeight() - vextent)
+ // {
+ // seqIndex = av.getAlignment().getHeight() - vextent;
+ // if (seqIndex < 0)
+ // {
+ // seqIndex = 0;
+ // }
+ // }
+ // setScrollValues(start, seqIndex);
+ // }
+ // logic copied from jalview.gui.AlignmentPanel:
+ if ((startv = vpRanges.getStartRes()) >= start)
+ {
+ /*
+ * Scroll left to make start of search results visible
+ */
+ setScrollValues(start - 1, seqIndex);
+ }
+ else if ((endv = vpRanges.getEndRes()) <= end)
+ {
+ /*
+ * Scroll right to make end of search results visible
+ */
+ setScrollValues(startv + 1 + end - endv, seqIndex);
+ }
+ else if ((starts = vpRanges.getStartSeq()) > seqIndex)
+ {
+ /*
+ * Scroll up to make start of search results visible
+ */
+ setScrollValues(vpRanges.getStartRes(), seqIndex);
+ }
+ else if ((ends = vpRanges.getEndSeq()) <= seqIndex)
+ {
+ /*
+ * Scroll down to make end of search results visible
+ */
+ setScrollValues(vpRanges.getStartRes(), starts + seqIndex - ends
+ + 1);
+ }
+ /*
+ * Else results are already visible - no need to scroll
+ */
}
else
{
@@ -411,10 +522,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
{
int cwidth = seqPanel.seqCanvas
.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
- if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
+ if (res <= vpRanges.getStartRes()
+ || res >= (vpRanges.getStartRes() + cwidth))
{
vscroll.setValue(res / cwidth);
- av.startRes = vscroll.getValue() * cwidth;
+ vpRanges.setStartRes(vscroll.getValue() * cwidth);
}
}
@@ -430,11 +542,16 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
public void setAnnotationVisible(boolean b)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
annotationSpaceFillerHolder.setVisible(b);
annotationPanelHolder.setVisible(b);
}
+ else
+ {
+ annotationSpaceFillerHolder.setVisible(false);
+ annotationPanelHolder.setVisible(false);
+ }
validate();
repaint();
}
@@ -443,13 +560,15 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
* automatically adjust annotation panel height for new annotation whilst
* ensuring the alignment is still visible.
*/
+ @Override
public void adjustAnnotationHeight()
{
// TODO: display vertical annotation scrollbar if necessary
// this is called after loading new annotation onto alignment
if (alignFrame.getSize().height == 0)
{
- System.out.println("NEEDS FIXING");
+ System.out
+ .println("adjustAnnotationHeight frame size zero NEEDS FIXING");
}
fontChanged();
validateAnnotationDimensions(true);
@@ -460,61 +579,68 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
}
/**
- * calculate the annotation dimensions and refresh slider values accordingly.
- * need to do repaints/notifys afterwards.
+ * Calculate the annotation dimensions and refresh slider values accordingly.
+ * Need to do repaints/notifys afterwards.
*/
protected void validateAnnotationDimensions(boolean adjustPanelHeight)
{
- boolean modified = false;
- int height = av.calcPanelHeight();
- int minsize = 0;
- if (hscroll.isVisible())
- {
- height += (minsize = hscroll.getPreferredSize().height);
- }
- if (apvscroll.isVisible())
- {
- minsize += apvscroll.getPreferredSize().height;
- }
- int mheight = height;
- Dimension d = sequenceHolderPanel.getSize(), e = idPanel.getSize();
- int seqandannot = d.height - scalePanelHolder.getSize().height;
- // sets initial preferred height
- if ((height + 40) > seqandannot / 2)
+ int rowHeight = av.getCharHeight();
+ int alignmentHeight = rowHeight * av.getAlignment().getHeight();
+ int annotationHeight = av.calcPanelHeight();
+
+ int mheight = annotationHeight;
+ Dimension d = sequenceHolderPanel.getSize();
+
+ int availableHeight = d.height - scalePanelHolder.getHeight();
+
+ if (adjustPanelHeight)
{
- height = seqandannot / 2;
+ /*
+ * If not enough vertical space, maximize annotation height while keeping
+ * at least two rows of alignment visible
+ */
+ if (annotationHeight + alignmentHeight > availableHeight)
+ {
+ annotationHeight = Math.min(annotationHeight, availableHeight - 2
+ * rowHeight);
+ }
}
- if (!adjustPanelHeight)
+ else
{
// maintain same window layout whilst updating sliders
- height = annotationPanelHolder.getSize().height;
+ annotationHeight = annotationPanelHolder.getSize().height;
}
- if (seqandannot - height < 5)
+ if (availableHeight - annotationHeight < 5)
{
- height = seqandannot;
+ annotationHeight = availableHeight;
}
- annotationPanel.setSize(new Dimension(d.width, height));
- alabels.setSize(new Dimension(e.width, height));
- annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
- annotationPanelHolder.setSize(new Dimension(d.width, height));
- seqPanelHolder.setSize(d.width, seqandannot - height);
+
+ annotationPanel.setSize(new Dimension(d.width, annotationHeight));
+ annotationPanelHolder.setSize(new Dimension(d.width, annotationHeight));
+ // seqPanelHolder.setSize(d.width, seqandannot - height);
seqPanel.seqCanvas
.setSize(d.width, seqPanel.seqCanvas.getSize().height);
+
+ Dimension e = idPanel.getSize();
+ alabels.setSize(new Dimension(e.width, annotationHeight));
+ annotationSpaceFillerHolder.setSize(new Dimension(e.width,
+ annotationHeight));
+
int s = apvscroll.getValue();
- if (s > mheight - height)
+ if (s > mheight - annotationHeight)
{
s = 0;
}
- apvscroll.setValues(s, height, 0, mheight);
- annotationPanel.setScrollOffset(apvscroll.getValue());
- alabels.setScrollOffset(apvscroll.getValue());
+ apvscroll.setValues(s, annotationHeight, 0, mheight);
+ annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+ alabels.setScrollOffset(apvscroll.getValue(), false);
}
public void setWrapAlignment(boolean wrap)
{
- av.startSeq = 0;
- av.startRes = 0;
+ vpRanges.setStartSeq(0);
+ vpRanges.setStartRes(0);
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
@@ -525,7 +651,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
annotationPanelHolder.setVisible(false);
annotationSpaceFillerHolder.setVisible(false);
}
- else if (av.showAnnotation)
+ else if (av.isShowAnnotation())
{
annotationPanelHolder.setVisible(true);
annotationSpaceFillerHolder.setVisible(true);
@@ -536,6 +662,7 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
fontChanged(); // This is so that the scalePanel is resized correctly
validate();
+ sequenceHolderPanel.validate();
repaint();
}
@@ -604,10 +731,10 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
{
x = 0;
}
- ;
- hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
- vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
+
+ hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
+ vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
if (hextent > width)
{
@@ -642,17 +769,11 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
x = 0;
}
- av.setStartSeq(y);
-
- int endSeq = y + vextent;
- if (endSeq > av.getAlignment().getHeight())
- {
- endSeq = av.getAlignment().getHeight();
- }
-
- av.setEndSeq(endSeq);
- av.setStartRes(x);
- av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
+ vpRanges.setStartSeq(y);
+ vpRanges.setEndSeq(y + vextent);
+ vpRanges.setStartRes(x);
+ vpRanges.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
+ .getCharWidth())) - 1);
hscroll.setValues(x, hextent, 0, width);
vscroll.setValues(y, vextent, 0, height);
@@ -665,15 +786,16 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
}
+ @Override
public void adjustmentValueChanged(AdjustmentEvent evt)
{
- int oldX = av.getStartRes();
- int oldY = av.getStartSeq();
+ int oldX = vpRanges.getStartRes();
+ int oldY = vpRanges.getStartSeq();
if (evt == null || evt.getSource() == apvscroll)
{
- annotationPanel.setScrollOffset(apvscroll.getValue());
- alabels.setScrollOffset(apvscroll.getValue());
+ annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+ alabels.setScrollOffset(apvscroll.getValue(), false);
// annotationPanel.image=null;
// alabels.image=null;
// alabels.repaint();
@@ -682,8 +804,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
if (evt == null || evt.getSource() == hscroll)
{
int x = hscroll.getValue();
- av.setStartRes(x);
- av.setEndRes(x + seqPanel.seqCanvas.getSize().width
+ vpRanges.setStartRes(x);
+ vpRanges.setEndRes(x + seqPanel.seqCanvas.getSize().width
/ av.getCharWidth() - 1);
}
@@ -694,14 +816,14 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
{
int rowSize = seqPanel.seqCanvas
.getWrappedCanvasWidth(seqPanel.seqCanvas.getSize().width);
- av.setStartRes(vscroll.getValue() * rowSize);
- av.setEndRes((vscroll.getValue() + 1) * rowSize);
+ vpRanges.setStartRes(vscroll.getValue() * rowSize);
+ vpRanges.setEndRes((vscroll.getValue() + 1) * rowSize);
}
else
{
- av.setStartSeq(offy);
- av.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
- / av.getCharHeight());
+ vpRanges.setStartSeq(offy);
+ vpRanges.setEndSeq(offy + seqPanel.seqCanvas.getSize().height
+ / av.getCharHeight() - 1);
}
}
@@ -710,8 +832,8 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
overviewPanel.setBoxPosition();
}
- int scrollX = av.startRes - oldX;
- int scrollY = av.startSeq - oldY;
+ int scrollX = vpRanges.getStartRes() - oldX;
+ int scrollY = vpRanges.getStartSeq() - oldY;
if (av.getWrapAlignment() || !fastPaint || av.MAC)
{
@@ -721,41 +843,138 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
{
// Make sure we're not trying to draw a panel
// larger than the visible window
- if (scrollX > av.endRes - av.startRes)
+ if (scrollX > vpRanges.getEndRes() - vpRanges.getStartRes())
{
- scrollX = av.endRes - av.startRes;
+ scrollX = vpRanges.getEndRes() - vpRanges.getStartRes();
}
- else if (scrollX < av.startRes - av.endRes)
+ else if (scrollX < vpRanges.getStartRes() - vpRanges.getEndRes())
{
- scrollX = av.startRes - av.endRes;
+ scrollX = vpRanges.getStartRes() - vpRanges.getEndRes();
}
idPanel.idCanvas.fastPaint(scrollY);
seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
scalePanel.repaint();
- if (av.getShowAnnotation())
+ if (av.isShowAnnotation())
{
- annotationPanel.fastPaint(av.getStartRes() - oldX);
+ annotationPanel.fastPaint(vpRanges.getStartRes() - oldX);
}
}
sendViewPosition();
+ /*
+ * If there is one, scroll the (Protein/cDNA) complementary alignment to
+ * match, unless we are ourselves doing that.
+ */
+ if (isFollowingComplementScroll())
+ {
+ setFollowingComplementScroll(false);
+ }
+ else
+ {
+ AlignmentPanel ap = getComplementPanel();
+ av.scrollComplementaryAlignment(ap);
+ }
+
+ }
+
+ /**
+ * A helper method to return the AlignmentPanel in the other (complementary)
+ * half of a SplitFrame view. Returns null if not in a SplitFrame.
+ *
+ * @return
+ */
+ private AlignmentPanel getComplementPanel()
+ {
+ AlignmentPanel ap = null;
+ if (alignFrame != null)
+ {
+ SplitFrame sf = alignFrame.getSplitFrame();
+ if (sf != null)
+ {
+ AlignFrame other = sf.getComplement(alignFrame);
+ if (other != null)
+ {
+ ap = other.alignPanel;
+ }
+ }
+ }
+ return ap;
+ }
+
+ /**
+ * Follow a scrolling change in the (cDNA/Protein) complementary alignment.
+ * The aim is to keep the two alignments 'lined up' on their centre columns.
+ *
+ * @param sr
+ * holds mapped region(s) of this alignment that we are scrolling
+ * 'to'; may be modified for sequence offset by this method
+ * @param seqOffset
+ * the number of visible sequences to show above the mapped region
+ */
+ protected void scrollToCentre(SearchResultsI sr, int seqOffset)
+ {
+ /*
+ * To avoid jumpy vertical scrolling (if some sequences are gapped or not
+ * mapped), we can make the scroll-to location a sequence above the one
+ * actually mapped.
+ */
+ SequenceI mappedTo = sr.getResults().get(0).getSequence();
+ List seqs = av.getAlignment().getSequences();
+
+ /*
+ * This is like AlignmentI.findIndex(seq) but here we are matching the
+ * dataset sequence not the aligned sequence
+ */
+ int sequenceIndex = 0;
+ boolean matched = false;
+ for (SequenceI seq : seqs)
+ {
+ if (mappedTo == seq.getDatasetSequence())
+ {
+ matched = true;
+ break;
+ }
+ sequenceIndex++;
+ }
+ if (!matched)
+ {
+ return; // failsafe, shouldn't happen
+ }
+
+ /*
+ * Scroll to position but centring the target residue. Also set a state flag
+ * to prevent adjustmentValueChanged performing this recursively.
+ */
+ setFollowingComplementScroll(true);
+ // this should be scrollToPosition(sr,verticalOffset,
+ scrollToPosition(sr, seqOffset, true, true);
}
private void sendViewPosition()
{
StructureSelectionManager.getStructureSelectionManager(av.applet)
- .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
- av.endSeq);
+ .sendViewPosition(this, vpRanges.getStartRes(),
+ vpRanges.getEndRes(), vpRanges.getStartSeq(),
+ vpRanges.getEndSeq());
}
+ /**
+ * Repaint the alignment and annotations, and, optionally, any overview window
+ */
+ @Override
public void paintAlignment(boolean updateOverview)
{
+ final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+ av.isShowAutocalculatedAbove());
+ sorter.sort(getAlignment().getAlignmentAnnotation(),
+ av.getSortAnnotationsBy());
repaint();
if (updateOverview)
{
+ // TODO: determine if this paintAlignment changed structure colours
jalview.structure.StructureSelectionManager
.getStructureSelectionManager(av.applet)
.sequenceColoursChanged(this);
@@ -767,16 +986,22 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
}
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
invalidate();
Dimension d = idPanel.idCanvas.getSize();
- idPanel.idCanvas.setSize(d.width, seqPanel.seqCanvas.getSize().height);
+ final int canvasHeight = seqPanel.seqCanvas.getSize().height;
+ if (canvasHeight != d.height)
+ {
+ idPanel.idCanvas.setSize(d.width, canvasHeight);
+ }
if (av.getWrapAlignment())
{
@@ -800,15 +1025,21 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
}
else
{
- setScrollValues(av.getStartRes(), av.getStartSeq());
+ setScrollValues(vpRanges.getStartRes(), vpRanges.getStartSeq());
}
- alabels.repaint();
-
seqPanel.seqCanvas.repaint();
- scalePanel.repaint();
- annotationPanel.repaint();
idPanel.idCanvas.repaint();
+ if (!av.getWrapAlignment())
+ {
+ if (av.isShowAnnotation())
+ {
+ alabels.repaint();
+ annotationPanel.repaint();
+ }
+ scalePanel.repaint();
+ }
+
}
protected Panel sequenceHolderPanel = new Panel();
@@ -819,72 +1050,58 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
protected Panel seqPanelHolder = new Panel();
- BorderLayout borderLayout1 = new BorderLayout();
-
- BorderLayout borderLayout3 = new BorderLayout();
-
protected Panel scalePanelHolder = new Panel();
protected Panel idPanelHolder = new Panel();
- BorderLayout borderLayout5 = new BorderLayout();
-
protected Panel idSpaceFillerPanel1 = new Panel();
public Panel annotationSpaceFillerHolder = new Panel();
- BorderLayout borderLayout6 = new BorderLayout();
-
- BorderLayout borderLayout7 = new BorderLayout();
-
- Panel hscrollHolder = new Panel();
-
- BorderLayout borderLayout10 = new BorderLayout();
-
protected Panel hscrollFillerPanel = new Panel();
- BorderLayout borderLayout11 = new BorderLayout();
-
- BorderLayout borderLayout4 = new BorderLayout();
-
- BorderLayout borderLayout2 = new BorderLayout();
-
Panel annotationPanelHolder = new Panel();
protected Scrollbar apvscroll = new Scrollbar();
- BorderLayout borderLayout12 = new BorderLayout();
+ /*
+ * Flag set while scrolling to follow complementary cDNA/protein scroll. When
+ * true, suppresses invoking the same method recursively.
+ */
+ private boolean followingComplementScroll;
private void jbInit() throws Exception
{
// idPanelHolder.setPreferredSize(new Dimension(70, 10));
- this.setLayout(borderLayout7);
+ this.setLayout(new BorderLayout());
// sequenceHolderPanel.setPreferredSize(new Dimension(150, 150));
- sequenceHolderPanel.setLayout(borderLayout3);
- seqPanelHolder.setLayout(borderLayout1);
+ sequenceHolderPanel.setLayout(new BorderLayout());
+ seqPanelHolder.setLayout(new BorderLayout());
scalePanelHolder.setBackground(Color.white);
// scalePanelHolder.setPreferredSize(new Dimension(10, 30));
- scalePanelHolder.setLayout(borderLayout6);
- idPanelHolder.setLayout(borderLayout5);
+ scalePanelHolder.setLayout(new BorderLayout());
+ idPanelHolder.setLayout(new BorderLayout());
idSpaceFillerPanel1.setBackground(Color.white);
// idSpaceFillerPanel1.setPreferredSize(new Dimension(10, 30));
- idSpaceFillerPanel1.setLayout(borderLayout11);
+ idSpaceFillerPanel1.setLayout(new BorderLayout());
annotationSpaceFillerHolder.setBackground(Color.white);
// annotationSpaceFillerHolder.setPreferredSize(new Dimension(10, 80));
- annotationSpaceFillerHolder.setLayout(borderLayout4);
+ annotationSpaceFillerHolder.setLayout(new BorderLayout());
hscroll.setOrientation(Scrollbar.HORIZONTAL);
- hscrollHolder.setLayout(borderLayout10);
+
+ Panel hscrollHolder = new Panel();
+ hscrollHolder.setLayout(new BorderLayout());
hscrollFillerPanel.setBackground(Color.white);
apvscroll.setOrientation(Scrollbar.VERTICAL);
apvscroll.setVisible(true);
apvscroll.addAdjustmentListener(this);
annotationPanelHolder.setBackground(Color.white);
- annotationPanelHolder.setLayout(borderLayout12);
+ annotationPanelHolder.setLayout(new BorderLayout());
annotationPanelHolder.add(apvscroll, BorderLayout.EAST);
// hscrollFillerPanel.setPreferredSize(new Dimension(70, 10));
hscrollHolder.setBackground(Color.white);
@@ -935,6 +1152,12 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
}
@Override
+ public String getViewName()
+ {
+ return getName();
+ }
+
+ @Override
public StructureSelectionManager getStructureSelectionManager()
{
return StructureSelectionManager
@@ -949,4 +1172,19 @@ public class AlignmentPanel extends Panel implements AdjustmentListener,
error.printStackTrace();
}
+ /**
+ * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
+ *
+ * @param b
+ */
+ protected void setFollowingComplementScroll(boolean b)
+ {
+ this.followingComplementScroll = b;
+ }
+
+ protected boolean isFollowingComplementScroll()
+ {
+ return this.followingComplementScroll;
+ }
+
}