/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
+ * Copyright (C) 2015 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 <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.awt.*;
-import java.awt.event.*;
-import java.util.Hashtable;
-import java.util.Vector;
-
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.*;
-
-public class AlignmentPanel extends Panel implements AdjustmentListener, AlignmentViewPanel
+import jalview.bin.JalviewLite;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
+
+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
{
public AlignViewport av;
// this value is set false when selection area being dragged
boolean fastPaint = true;
+ public void finalize()
+ {
+ alignFrame = null;
+ av = null;
+ seqPanel = null;
+ seqPanelHolder = null;
+ sequenceHolderPanel = null;
+ scalePanel = null;
+ scalePanelHolder = null;
+ annotationPanel = null;
+ annotationPanelHolder = null;
+ annotationSpaceFillerHolder = null;
+ }
+
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
try
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);
public void componentResized(ComponentEvent evt)
{
setScrollValues(av.getStartRes(), av.getStartSeq());
+ if (getSize().height > 0
+ && annotationPanelHolder.getSize().height > 0)
+ {
+ validateAnnotationDimensions(false);
+ }
repaint();
}
+
});
Dimension d = calculateIdWidth();
}
}
});
+ }
+ @Override
+ public AlignViewportI getAlignViewport()
+ {
+ return av;
}
public SequenceRenderer getSequenceRenderer()
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);
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;
Dimension d = calculateIdWidth();
d.setSize(d.width + 4, seqPanel.seqCanvas.getSize().height);
alabels.setSize(d.width + 4, ap);
+
idPanel.idCanvas.setSize(d);
hscrollFillerPanel.setSize(d);
-
+
validateAnnotationDimensions(false);
annotationPanel.repaint();
validate();
{
idPanel.idCanvas.setSize(w, h);
idPanelHolder.setSize(w, idPanelHolder.getSize().height);
- annotationSpaceFillerHolder.setSize(w,annotationSpaceFillerHolder.getSize().height);
+ annotationSpaceFillerHolder.setSize(w,
+ annotationSpaceFillerHolder.getSize().height);
alabels.setSize(w, alabels.getSize().height);
validate();
}
public boolean scrollToPosition(SearchResults results,
boolean redrawOverview)
{
+ return scrollToPosition(results, 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(SearchResults results,
+ boolean redrawOverview, boolean centre)
+ {
// do we need to scroll the panel?
if (results != null && results.getSize() > 0)
{
- int seqIndex = av.alignment.findIndex(results);
+ AlignmentI alignment = av.getAlignment();
+ int seqIndex = alignment.findIndex(results);
if (seqIndex == -1)
{
return false;
}
- SequenceI seq = av.alignment.getSequenceAt(seqIndex);
- int[] r = results.getResults(seq, 0,av.alignment.getWidth());
+ SequenceI seq = alignment.getSequenceAt(seqIndex);
+ int[] r = results.getResults(seq, 0, alignment.getWidth());
if (r == null)
{
- if (av.applet.debug) {// DEBUG
- System.out.println("DEBUG: scroll didn't happen - results not within alignment : "+seq.getStart()+","+seq.getEnd());
+ if (JalviewLite.debug)
+ {// DEBUG
+ System.out
+ .println("DEBUG: scroll didn't happen - results not within alignment : "
+ + seq.getStart() + "," + seq.getEnd());
}
return false;
}
- if (av.applet.debug) {
+ if (JalviewLite.debug)
+ {
// DEBUG
- System.out.println("DEBUG: scroll didn't happen: start=" + r[0]
- + " av.getStartRes()=" + av.getStartRes() + " end=" + r[1]
- + " seq.end=" + seq.getEnd() + " av.getEndRes()="
- + av.getEndRes() + " hextent=" + hextent);
+ /*
+ * System.out.println("DEBUG: scroll: start=" + r[0] +
+ * " av.getStartRes()=" + av.getStartRes() + " end=" + r[1] +
+ * " seq.end=" + seq.getEnd() + " av.getEndRes()=" + av.getEndRes() +
+ * " hextent=" + hextent);
+ */
}
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 = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1;
+ start = Math.max(start - offset, 0);
+ end = Math.min(end + offset, seq.getEnd() - 1);
+ }
+
if (start < 0)
{
return false;
{
return false;
}
- if (av.hasHiddenColumns)
+ return scrollTo(start, end, seqIndex, false, redrawOverview);
+ }
+ return true;
+ }
+
+ public boolean scrollTo(int ostart, int end, int seqIndex,
+ boolean scrollToNearest, boolean redrawOverview)
+ {
+ int startv, endv, starts, ends, width;
+
+ int start = -1;
+ if (av.hasHiddenColumns())
+ {
+ start = av.getColumnSelection().findColumnPosition(ostart);
+ end = av.getColumnSelection().findColumnPosition(end);
+ if (start == end)
{
- start = av.getColumnSelection().findColumnPosition(start);
- end = av.getColumnSelection().findColumnPosition(end);
- if (start == end)
+ if (!scrollToNearest && !av.getColumnSelection().isVisible(ostart))
{
- if (!av.colSel.isVisible(r[0]))
- {
- // don't scroll - position isn't visible
- return false;
- }
+ // don't scroll - position isn't visible
+ return false;
}
}
- if (!av.wrapAlignment)
+ }
+ else
+ {
+ start = ostart;
+ }
+ if (!av.getWrapAlignment())
+ {
+ /*
+ * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv =
+ * av.getStartRes()) >= start) { spos=start-1; // seqIn //
+ * setScrollValues(start - 1, seqIndex); } else if ((endv =
+ * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end -
+ * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts =
+ * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(),
+ * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) {
+ * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); }
+ */
+
+ // 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 = av.getStartRes()) >= start)
{
- if ((av.getStartRes() > end)
- || (av.getEndRes() < start)
- || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
- {
- if (start > av.alignment.getWidth() - hextent)
- {
- start = av.alignment.getWidth() - hextent;
- if (start < 0)
- {
- start = 0;
- }
-
- }
- if (seqIndex > av.alignment.getHeight() - vextent)
- {
- seqIndex = av.alignment.getHeight() - vextent;
- if (seqIndex < 0)
- {
- seqIndex = 0;
- }
- }
- setScrollValues(start, seqIndex);
- }
+ /*
+ * Scroll left to make start of search results visible
+ */
+ setScrollValues(start - 1, seqIndex);
}
- else
+ else if ((endv = av.getEndRes()) <= end)
+ {
+ /*
+ * Scroll right to make end of search results visible
+ */
+ setScrollValues(startv + 1 + end - endv, seqIndex);
+ }
+ else if ((starts = av.getStartSeq()) > seqIndex)
{
- scrollToWrappedVisible(start);
+ /*
+ * Scroll up to make start of search results visible
+ */
+ setScrollValues(av.getStartRes(), seqIndex);
}
+ else if ((ends = av.getEndSeq()) <= seqIndex)
+ {
+ /*
+ * Scroll down to make end of search results visible
+ */
+ setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
+ }
+ /*
+ * Else results are already visible - no need to scroll
+ */
+ }
+ else
+ {
+ scrollToWrappedVisible(start);
}
if (redrawOverview && overviewPanel != null)
{
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();
}
+ /**
+ * automatically adjust annotation panel height for new annotation whilst
+ * ensuring the alignment is still visible.
+ */
+ 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("adjustAnnotationHeight frame size zero NEEDS FIXING");
+ }
+ fontChanged();
+ validateAnnotationDimensions(true);
+ apvscroll.addNotify();
+ hscroll.addNotify();
+ validate();
+ paintAlignment(true);
+ }
+
+ /**
+ * Calculate the annotation dimensions and refresh slider values accordingly.
+ * Need to do repaints/notifys afterwards.
+ */
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight)
+ {
+ 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)
+ {
+ /*
+ * 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);
+ }
+ }
+ else
+ {
+ // maintain same window layout whilst updating sliders
+ annotationHeight = annotationPanelHolder.getSize().height;
+ }
+
+ if (availableHeight - annotationHeight < 5)
+ {
+ annotationHeight = availableHeight;
+ }
+
+ 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 - annotationHeight)
+ {
+ s = 0;
+ }
+ apvscroll.setValues(s, annotationHeight, 0, mheight);
+ annotationPanel.setScrollOffset(apvscroll.getValue(), false);
+ alabels.setScrollOffset(apvscroll.getValue(), false);
+ }
+
public void setWrapAlignment(boolean wrap)
{
av.startSeq = 0;
annotationPanelHolder.setVisible(false);
annotationSpaceFillerHolder.setVisible(false);
}
- else if (av.showAnnotation)
+ else if (av.isShowAnnotation())
{
annotationPanelHolder.setVisible(true);
annotationSpaceFillerHolder.setVisible(true);
fontChanged(); // This is so that the scalePanel is resized correctly
validate();
+ sequenceHolderPanel.validate();
repaint();
}
public void setScrollValues(int x, int y)
{
- int width = av.alignment.getWidth();
- int height = av.alignment.getHeight();
+ int width = av.getAlignment().getWidth();
+ int height = av.getAlignment().getHeight();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
width = av.getColumnSelection().findColumnPosition(width);
}
+ if (x < 0)
+ {
+ x = 0;
+ }
+ ;
- av.setStartRes(x);
- av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av.charWidth)) - 1);
+ hextent = seqPanel.seqCanvas.getSize().width / av.getCharWidth();
+ vextent = seqPanel.seqCanvas.getSize().height / av.getCharHeight();
- hextent = seqPanel.seqCanvas.getSize().width / av.charWidth;
- vextent = seqPanel.seqCanvas.getSize().height / av.charHeight;
-
if (hextent > width)
{
hextent = width;
if ((hextent + x) > width)
{
+ System.err.println("hextent was " + hextent + " and x was " + x);
+
x = width - hextent;
}
if (x < 0)
{
+ System.err.println("x was " + x);
x = 0;
}
av.setStartSeq(y);
int endSeq = y + vextent;
- if (endSeq > av.alignment.getHeight())
+ if (endSeq > av.getAlignment().getHeight())
{
- endSeq = av.alignment.getHeight();
+ endSeq = av.getAlignment().getHeight();
}
av.setEndSeq(endSeq);
+ av.setStartRes(x);
+ av.setEndRes((x + (seqPanel.seqCanvas.getSize().width / av
+ .getCharWidth())) - 1);
+
hscroll.setValues(x, hextent, 0, width);
vscroll.setValues(y, vextent, 0, height);
{
overviewPanel.setBoxPosition();
}
+ sendViewPosition();
}
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();
seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
scalePanel.repaint();
- if (av.getShowAnnotation())
+ if (av.isShowAnnotation())
{
annotationPanel.fastPaint(av.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(SearchResults 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.getResultSequence(0);
+ List<SequenceI> 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
+ }
+ sequenceIndex = Math.max(0, sequenceIndex - seqOffset);
+ sr.getResults().get(0)
+ .setSequence(av.getAlignment().getSequenceAt(sequenceIndex));
+
+ /*
+ * Scroll to position but centring the target residue. Also set a state flag
+ * to prevent adjustmentValueChanged performing this recursively.
+ */
+ setFollowingComplementScroll(true);
+ scrollToPosition(sr, true, true);
+ }
+
+ private void sendViewPosition()
+ {
+ StructureSelectionManager.getStructureSelectionManager(av.applet)
+ .sendViewPosition(this, av.startRes, av.endRes, av.startSeq,
+ av.endSeq);
}
+ /**
+ * Repaint the alignment and annotations, and, optionally, any overview window
+ */
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().sequenceColoursChanged(this);
+ .getStructureSelectionManager(av.applet)
+ .sequenceColoursChanged(this);
if (overviewPanel != null)
{
{
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())
{
- int maxwidth = av.alignment.getWidth();
+ int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
setScrollValues(av.getStartRes(), av.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();
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.setPreferredSize(new Dimension(150, 150));
+ 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);
public void updateAnnotation(boolean applyGlobalSettings)
{
- // TODO: this should be merged with other annotation update stuff - that
- // sits on AlignViewport
- boolean updateCalcs = false;
- boolean conv = av.isShowGroupConservation();
- boolean cons = av.isShowGroupConsensus();
- boolean showprf = av.isShowSequenceLogo();
- boolean showConsHist = av.isShowConsensusHistogram();
+ updateAnnotation(applyGlobalSettings, false);
+ }
- boolean sortg = true;
+ public void updateAnnotation(boolean applyGlobalSettings,
+ boolean preserveNewGroupSettings)
+ {
+ av.updateGroupAnnotationSettings(applyGlobalSettings,
+ preserveNewGroupSettings);
+ adjustAnnotationHeight();
+ }
- // remove old automatic annotation
- // add any new annotation
+ @Override
+ public AlignmentI getAlignment()
+ {
+ return av.getAlignment();
+ }
- Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
- // intersect alignment annotation with alignment groups
+ @Override
+ public String getViewName()
+ {
+ return getName();
+ }
- AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
- Hashtable oldrfs = new Hashtable();
- if (aan != null)
- {
- for (int an = 0; an < aan.length; an++)
- {
- if (aan[an].autoCalculated && aan[an].groupRef != null)
- {
- oldrfs.put(aan[an].groupRef, aan[an].groupRef);
- av.alignment.deleteAnnotation(aan[an]);
- aan[an] = null;
- }
- }
- }
- SequenceGroup sg;
- if (gr != null)
- {
- for (int g = 0; g < gr.size(); g++)
- {
- updateCalcs = false;
- sg = (SequenceGroup) gr.elementAt(g);
- if (applyGlobalSettings || !oldrfs.containsKey(sg))
- {
- // set defaults for this group's conservation/consensus
- sg.setshowSequenceLogo(showprf);
- sg.setShowConsensusHistogram(showConsHist);
- }
- if (conv)
- {
- updateCalcs = true;
- av.alignment.addAnnotation(sg.getConservationRow(), 0);
- }
- if (cons)
- {
- updateCalcs = true;
- av.alignment.addAnnotation(sg.getConsensus(), 0);
- }
- // refresh the annotation rows
- if (updateCalcs)
- {
- sg.recalcConservation();
- }
- }
- }
- oldrfs.clear();
- adjustAnnotationHeight();
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return StructureSelectionManager
+ .getStructureSelectionManager(av.applet);
}
- /**
- * automatically adjust annotation panel height for new annotation whilst
- * ensuring the alignment is still visible.
- */
- public void adjustAnnotationHeight()
+ @Override
+ public void raiseOOMWarning(String string, OutOfMemoryError error)
{
- // 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");
- }
- fontChanged();
- validateAnnotationDimensions(true);
- apvscroll.addNotify();
- hscroll.addNotify();
- validate();
- addNotify();
- repaint();
+ // TODO: JAL-960
+ System.err.println("Out of memory whilst '" + string + "'");
+ error.printStackTrace();
}
+
/**
- * calculate the annotation dimensions and refresh slider values accordingly.
- * need to do repaints/notifys afterwards.
+ * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
+ *
+ * @param b
*/
- protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
- int height = annotationPanel.calcPanelHeight();
- if (hscroll.isVisible())
- {
- height += hscroll.getPreferredSize().height;
- }
- int mheight = height;
- // sets initial preferred height
- if ((height+40) > getSize().height / 2)
- {
- height = getSize().height / 2;
- }
- if (!adjustPanelHeight)
- {
- // maintain same window layout whilst updating sliders
- height=seqPanelHolder.getSize().height;
- }
- Dimension d=seqPanelHolder.getSize(),e=idPanel.getSize();
- annotationPanel.setSize(new Dimension(d.width,height));
- alabels.setSize(e.width,height);
- annotationSpaceFillerHolder.setSize(new Dimension(e.width, height));
- annotationPanelHolder.setSize(new Dimension(d.width, height));
- seqPanelHolder.setSize(d.width,d.height-height);
- int s=apvscroll.getValue();
- if (s>mheight-height)
- {
- s = 0;
- }
- apvscroll.setValues(apvscroll.getValue(), height, 0, mheight);
- annotationPanel.setScrollOffset(apvscroll.getValue());
- alabels.setScrollOffset(apvscroll.getValue());
+ protected void setFollowingComplementScroll(boolean b)
+ {
+ this.followingComplementScroll = b;
}
- @Override
- public AlignmentI getAlignment()
+ protected boolean isFollowingComplementScroll()
{
- return av.alignment;
+ return this.followingComplementScroll;
}
}
git://source.jalview.org / jalview.git / blobdiff