/*
- * 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 <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.gui;
-import java.beans.*;
-import java.io.*;
-import java.util.Hashtable;
-import java.util.Vector;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import javax.swing.*;
-
+import jalview.analysis.AnnotationSorter;
+import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
+import jalview.bin.Console;
+import jalview.bin.Jalview;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SearchResultsI;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.io.HTMLOutput;
+import jalview.jbgui.GAlignmentPanel;
+import jalview.math.AlignmentDimension;
+import jalview.schemes.ResidueProperties;
import jalview.structure.StructureSelectionManager;
+import jalview.util.Comparison;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.viewmodel.ViewportListenerI;
+import jalview.viewmodel.ViewportRanges;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+import java.awt.event.ComponentAdapter;
+import java.awt.event.ComponentEvent;
+import java.awt.print.PageFormat;
+import java.awt.print.Printable;
+import java.awt.print.PrinterException;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.PrintWriter;
+import java.util.List;
+
+import javax.swing.SwingUtilities;
/**
* DOCUMENT ME!
* @author $author$
* @version $Revision: 1.161 $
*/
+@SuppressWarnings("serial")
public class AlignmentPanel extends GAlignmentPanel implements
- AdjustmentListener, Printable, AlignmentViewPanel
+ AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI
{
+ /*
+ * spare space in pixels between sequence id and alignment panel
+ */
+ private static final int ID_WIDTH_PADDING = 4;
+
public AlignViewport av;
OverviewPanel overviewPanel;
- SeqPanel seqPanel;
+ private SeqPanel seqPanel;
- IdPanel idPanel;
+ private IdPanel idPanel;
IdwidthAdjuster idwidthAdjuster;
- /** DOCUMENT ME!! */
public AlignFrame alignFrame;
- ScalePanel scalePanel;
+ private ScalePanel scalePanel;
+
+ private AnnotationPanel annotationPanel;
- AnnotationPanel annotationPanel;
+ private AnnotationLabels alabels;
- AnnotationLabels alabels;
+ private int hextent = 0;
- // this value is set false when selection area being dragged
- boolean fastPaint = true;
+ private int vextent = 0;
+
+ /*
+ * Flag set while scrolling to follow complementary cDNA/protein scroll. When
+ * false, suppresses invoking the same method recursively.
+ */
+ private boolean scrollComplementaryPanel = true;
- int hextent = 0;
+ private PropertyChangeListener propertyChangeListener;
- int vextent = 0;
+ private CalculationChooser calculationDialog;
/**
* Creates a new AlignmentPanel object.
*
* @param af
- * DOCUMENT ME!
* @param av
- * DOCUMENT ME!
*/
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
+// setBackground(Color.white); // BH 2019
alignFrame = af;
this.av = av;
- seqPanel = new SeqPanel(av, this);
- idPanel = new IdPanel(av, this);
+ setSeqPanel(new SeqPanel(av, this));
+ setIdPanel(new IdPanel(av, this));
- scalePanel = new ScalePanel(av, this);
+ setScalePanel(new ScalePanel(av, this));
- idPanelHolder.add(idPanel, BorderLayout.CENTER);
+ idPanelHolder.add(getIdPanel(), BorderLayout.CENTER);
idwidthAdjuster = new IdwidthAdjuster(this);
idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER);
- annotationPanel = new AnnotationPanel(this);
- alabels = new AnnotationLabels(this);
+ setAnnotationPanel(new AnnotationPanel(this));
+ setAlabels(new AnnotationLabels(this));
- annotationScroller.setViewportView(annotationPanel);
- annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER);
+ annotationScroller.setViewportView(getAnnotationPanel());
+ annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER);
- scalePanelHolder.add(scalePanel, BorderLayout.CENTER);
- seqPanelHolder.add(seqPanel, BorderLayout.CENTER);
+ scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER);
+ seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER);
setScrollValues(0, 0);
- setAnnotationVisible(av.getShowAnnotation());
-
hscroll.addAdjustmentListener(this);
vscroll.addAdjustmentListener(this);
+ addComponentListener(new ComponentAdapter()
+ {
+ @Override
+ public void componentResized(ComponentEvent evt)
+ {
+ // reset the viewport ranges when the alignment panel is resized
+ // in particular, this initialises the end residue value when Jalview
+ // is initialised
+ ViewportRanges ranges = av.getRanges();
+ if (av.getWrapAlignment())
+ {
+ int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth(
+ getSeqPanel().seqCanvas.getWidth());
+ ranges.setViewportWidth(widthInRes);
+ }
+ else
+ {
+ int widthInRes = getSeqPanel().seqCanvas.getWidth()
+ / av.getCharWidth();
+ int heightInSeq = getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight();
+
+ ranges.setViewportWidth(widthInRes);
+ ranges.setViewportHeight(heightInSeq);
+ }
+ }
+
+ });
+
final AlignmentPanel ap = this;
- av.addPropertyChangeListener(new PropertyChangeListener()
+ propertyChangeListener = new PropertyChangeListener()
{
+ @Override
public void propertyChange(PropertyChangeEvent evt)
{
if (evt.getPropertyName().equals("alignment"))
alignmentChanged();
}
}
- });
+ };
+ av.addPropertyChangeListener(propertyChangeListener);
+
+ av.getRanges().addPropertyChangeListener(this);
fontChanged();
adjustAnnotationHeight();
+ updateLayout();
+ }
+ @Override
+ public AlignViewportI getAlignViewport()
+ {
+ return av;
}
public void alignmentChanged()
{
av.alignmentChanged(this);
+ if (getCalculationDialog() != null)
+ {
+ getCalculationDialog().validateCalcTypes();
+ }
+
alignFrame.updateEditMenuBar();
- paintAlignment(true);
+ // no idea if we need to update structure
+ paintAlignment(true, true);
}
// to prevent drawing old image
FontMetrics fm = getFontMetrics(av.getFont());
- scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight
- + fm.getDescent()));
- idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight
- + fm.getDescent()));
-
- idPanel.idCanvas.gg = null;
- seqPanel.seqCanvas.img = null;
- annotationPanel.adjustPanelHeight();
+ scalePanelHolder.setPreferredSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
+ idSpaceFillerPanel1.setPreferredSize(
+ new Dimension(10, av.getCharHeight() + fm.getDescent()));
+ idwidthAdjuster.invalidate();
+ scalePanelHolder.invalidate();
+ // BH 2018 getIdPanel().getIdCanvas().gg = null;
+ getSeqPanel().seqCanvas.img = null;
+ getAnnotationPanel().adjustPanelHeight();
Dimension d = calculateIdWidth();
- d.setSize(d.width + 4, d.height);
- idPanel.idCanvas.setPreferredSize(d);
+ getIdPanel().getIdCanvas().setPreferredSize(d);
hscrollFillerPanel.setPreferredSize(d);
- if (overviewPanel != null)
- {
- overviewPanel.setBoxPosition();
- }
-
repaint();
}
/**
- * Calculate the width of the alignment labels based on the displayed names
- * and any bounds on label width set in preferences.
+ * Calculates the width of the alignment labels based on the displayed names
+ * and any bounds on label width set in preferences. The calculated width is
+ * also set as a property of the viewport.
*
* @return Dimension giving the maximum width of the alignment label panel
* that should be used.
*/
public Dimension calculateIdWidth()
{
+ int oldWidth = av.getIdWidth();
+
// calculate sensible default width when no preference is available
-
- int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
- int maxwidth = Math.max(20,
- Math.min(afwidth - 200, (int) 2 * afwidth / 3));
- return calculateIdWidth(maxwidth);
+ Dimension r = null;
+ if (av.getIdWidth() < 0)
+ {
+ int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+ int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
+ int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
+ r = calculateIdWidth(maxwidth);
+ av.setIdWidth(r.width);
+ }
+ else
+ {
+ r = new Dimension();
+ r.width = av.getIdWidth();
+ r.height = 0;
+ }
+
+ /*
+ * fudge: if desired width has changed, update layout
+ * (see also paintComponent - updates layout on a repaint)
+ */
+ if (r.width != oldWidth)
+ {
+ idPanelHolder.setPreferredSize(r);
+ validate();
+ }
+ return r;
}
+
/**
* Calculate the width of the alignment labels based on the displayed names
* and any bounds on label width set in preferences.
- * @param maxwidth -1 or maximum width allowed for IdWidth
+ *
+ * @param maxwidth
+ * -1 or maximum width allowed for IdWidth
* @return Dimension giving the maximum width of the alignment label panel
* that should be used.
*/
- public Dimension calculateIdWidth(int maxwidth)
+ protected Dimension calculateIdWidth(int maxwidth)
{
Container c = new Container();
- FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(),
- Font.ITALIC, av.font.getSize()));
+ FontMetrics fm = c.getFontMetrics(
+ new Font(av.font.getName(), Font.ITALIC, av.font.getSize()));
AlignmentI al = av.getAlignment();
int i = 0;
int idWidth = 0;
- String id;
while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
{
SequenceI s = al.getSequenceAt(i);
-
- id = s.getDisplayId(av.getShowJVSuffix());
-
- if (fm.stringWidth(id) > idWidth)
- {
- idWidth = fm.stringWidth(id);
- }
-
+ String id = s.getDisplayId(av.getShowJVSuffix());
+ int stringWidth = fm.stringWidth(id);
+ idWidth = Math.max(idWidth, stringWidth);
i++;
}
if (al.getAlignmentAnnotation() != null)
{
- fm = c.getFontMetrics(alabels.getFont());
+ fm = c.getFontMetrics(getAlabels().getFont());
while (i < al.getAlignmentAnnotation().length)
{
String label = al.getAlignmentAnnotation()[i].label;
-
- if (fm.stringWidth(label) > idWidth)
- {
- idWidth = fm.stringWidth(label);
- }
-
+ int stringWidth = fm.stringWidth(label);
+ idWidth = Math.max(idWidth, stringWidth);
i++;
}
}
- return new Dimension(maxwidth<0 ? idWidth : Math.min(maxwidth, idWidth), 12);
+ int w = maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth);
+ w += ID_WIDTH_PADDING;
+
+ return new Dimension(w, 12);
}
/**
- * Highlight the given results on the alignment.
+ * Highlight the given results on the alignment
*
*/
- public void highlightSearchResults(SearchResults results)
+ public void highlightSearchResults(SearchResultsI results)
{
- scrollToPosition(results);
- seqPanel.seqCanvas.highlightSearchResults(results);
+ boolean scrolled = scrollToPosition(results, 0, false);
+
+ boolean fastPaint = !(scrolled && av.getWrapAlignment());
+
+ getSeqPanel().seqCanvas.highlightSearchResults(results, fastPaint);
}
/**
- * scroll the view to show the position of the highlighted region in results
- * (if any) and redraw the overview
+ * Scroll the view to show the position of the highlighted region in results
+ * (if any)
*
- * @param results
+ * @param searchResults
+ * @return
*/
- public boolean scrollToPosition(SearchResults results)
+ public boolean scrollToPosition(SearchResultsI searchResults)
{
- return scrollToPosition(results, true);
+ return scrollToPosition(searchResults, 0, false);
}
/**
- * scroll the view to show the position of the highlighted region in results
- * (if any)
+ * Scrolls the view (if necessary) to show the position of the first
+ * highlighted region in results (if any). Answers true if the view was
+ * scrolled, or false if no matched region was found, or it is already
+ * visible.
*
* @param results
- * @param redrawOverview
- * - when set, the overview will be recalculated (takes longer)
- * @return false if results were not found
+ * @param verticalOffset
+ * if greater than zero, allows scrolling to a position below the
+ * first displayed sequence
+ * @param centre
+ * if true, try to centre the search results horizontally in the view
+ * @return
*/
- public boolean scrollToPosition(SearchResults results,
- boolean redrawOverview)
+ protected boolean scrollToPosition(SearchResultsI results,
+ int verticalOffset, boolean centre)
{
- int startv, endv, starts, ends, width;
- // TODO: properly locate search results in view when large numbers of hidden
- // columns exist before highlighted region
- // do we need to scroll the panel?
- // TODO: tons of nullpointereexceptions raised here.
- if (results != null && results.getSize() > 0 && av != null
- && av.getAlignment() != null)
+ int startv, endv, starts, ends;
+ ViewportRanges ranges = av.getRanges();
+
+ if (results == null || results.isEmpty() || av == null
+ || av.getAlignment() == null)
{
- int seqIndex = av.getAlignment().findIndex(results);
- if (seqIndex == -1)
- {
- return false;
- }
- SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
-
- int[] r=results.getResults(seq, 0, av.getAlignment().getWidth());
- if (r == null)
- {
- return false;
- }
- int start = r[0];
- int end = r[1];
- // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
- // DEBUG
- if (start < 0)
+ return false;
+ }
+ int seqIndex = av.getAlignment().findIndex(results);
+ if (seqIndex == -1)
+ {
+ return false;
+ }
+ SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
+
+ int[] r = results.getResults(seq, 0, av.getAlignment().getWidth());
+ if (r == null)
+ {
+ return false;
+ }
+ 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 = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1;
+ start = Math.max(start - offset, 0);
+ end = end + offset - 1;
+ }
+ if (start < 0)
+ {
+ return false;
+ }
+ if (end == seq.getEnd())
+ {
+ return false;
+ }
+
+ if (av.hasHiddenColumns())
+ {
+ HiddenColumns hidden = av.getAlignment().getHiddenColumns();
+ start = hidden.absoluteToVisibleColumn(start);
+ end = hidden.absoluteToVisibleColumn(end);
+ if (start == end)
{
- return false;
+ if (!hidden.isVisible(r[0]))
+ {
+ // don't scroll - position isn't visible
+ return false;
+ }
}
- if (end == seq.getEnd())
+ }
+
+ /*
+ * allow for offset of target sequence (actually scroll to one above it)
+ */
+ seqIndex = Math.max(0, seqIndex - verticalOffset);
+ boolean scrollNeeded = true;
+
+ if (!av.getWrapAlignment())
+ {
+ if ((startv = ranges.getStartRes()) >= start)
{
- return false;
+ /*
+ * Scroll left to make start of search results visible
+ */
+ setScrollValues(start, seqIndex);
}
- if (av.hasHiddenColumns())
+ else if ((endv = ranges.getEndRes()) <= end)
{
- start = av.getColumnSelection().findColumnPosition(start);
- end = av.getColumnSelection().findColumnPosition(end);
- if (start==end)
- {
- if (!av.getColumnSelection().isVisible(r[0]))
- {
- // don't scroll - position isn't visible
- return false;
- }
- }
+ /*
+ * Scroll right to make end of search results visible
+ */
+ setScrollValues(startv + end - endv, seqIndex);
}
- if (!av.wrapAlignment)
+ else if ((starts = ranges.getStartSeq()) > seqIndex)
{
- if ((startv = av.getStartRes()) >= start)
- {
- setScrollValues(start - 1, seqIndex);
- }
- else if ((endv = av.getEndRes()) <= end)
- {
- setScrollValues(startv + 1 + end - endv, seqIndex);
- }
- else if ((starts = av.getStartSeq()) > seqIndex)
- {
- setScrollValues(av.getStartRes(), seqIndex);
- }
- else if ((ends = av.getEndSeq()) <= seqIndex)
- {
- setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1);
- }
+ /*
+ * Scroll up to make start of search results visible
+ */
+ setScrollValues(ranges.getStartRes(), seqIndex);
}
- else
+ else if ((ends = ranges.getEndSeq()) <= seqIndex)
{
- scrollToWrappedVisible(start);
+ /*
+ * Scroll down to make end of search results visible
+ */
+ setScrollValues(ranges.getStartRes(), starts + seqIndex - ends
+ + 1);
}
+ /*
+ * Else results are already visible - no need to scroll
+ */
+ scrollNeeded = false;
}
- if (redrawOverview && overviewPanel != null)
+ else
{
- overviewPanel.setBoxPosition();
+ scrollNeeded = ranges.scrollToWrappedVisible(start);
}
- paintAlignment(redrawOverview);
- return true;
- }
- void scrollToWrappedVisible(int res)
- {
- int cwidth = seqPanel.seqCanvas
- .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
- if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
- {
- vscroll.setValue((res / cwidth));
- av.startRes = vscroll.getValue() * cwidth;
- }
+ paintAlignment(false, false);
+ return scrollNeeded;
}
/**
/**
*
- * @param b Hide or show annotation panel
- *
+ * @param b
+ * Hide or show annotation panel
+ *
*/
public void setAnnotationVisible(boolean b)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
annotationSpaceFillerHolder.setVisible(b);
annotationScroller.setVisible(b);
}
/**
- * automatically adjust annotation panel height for new annotation
- * whilst ensuring the alignment is still visible.
+ * 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
}
validateAnnotationDimensions(true);
addNotify();
- paintAlignment(true);
+ // TODO: many places call this method and also paintAlignment with various
+ // different settings. this means multiple redraws are triggered...
+ paintAlignment(true, av.needToUpdateStructureViews());
}
+
/**
* calculate the annotation dimensions and refresh slider values accordingly.
- * need to do repaints/notifys afterwards.
+ * need to do repaints/notifys afterwards.
*/
- protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
- int height = annotationPanel.adjustPanelHeight();
-
- if (hscroll.isVisible())
- {
- height += hscroll.getPreferredSize().height;
- }
- if (height > alignFrame.getHeight() / 2)
- {
- height = alignFrame.getHeight() / 2;
- }
- if (!adjustPanelHeight)
- {
- // maintain same window layout whilst updating sliders
- height=annotationScroller.getSize().height;
- }
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight)
+ {
+ // BH 2018.04.18 comment: addNotify() is not appropriate here. We
+ // are not changing ancestors, and keyboard action listeners do
+ // not need to be reset. addNotify() is a very expensive operation,
+ // requiring a full re-layout of all parents and children.
+ // Note in JComponent:
+ // This method is called by the toolkit internally and should
+ // not be called directly by programs.
+ // I note that addNotify() is called in several areas of Jalview.
+
+ int annotationHeight = getAnnotationPanel().adjustPanelHeight();
+ annotationHeight = getAnnotationPanel()
+ .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
+
hscroll.addNotify();
-
- annotationScroller.setPreferredSize(new Dimension(annotationScroller
- .getWidth(), height));
+ annotationScroller.setPreferredSize(
+ new Dimension(annotationScroller.getWidth(), annotationHeight));
+
+ Dimension e = idPanel.getSize();
+ alabels.setSize(new Dimension(e.width, annotationHeight));
+
annotationSpaceFillerHolder.setPreferredSize(new Dimension(
- annotationSpaceFillerHolder.getWidth(), height));
- annotationScroller.validate();// repaint();
+ annotationSpaceFillerHolder.getWidth(), annotationHeight));
+ annotationScroller.validate();
annotationScroller.addNotify();
}
/**
- * DOCUMENT ME!
+ * update alignment layout for viewport settings
*
* @param wrap
* DOCUMENT ME!
*/
- public void setWrapAlignment(boolean wrap)
+ public void updateLayout()
{
- av.startSeq = 0;
+ fontChanged();
+ setAnnotationVisible(av.isShowAnnotation());
+ boolean wrap = av.getWrapAlignment();
+ ViewportRanges ranges = av.getRanges();
+ ranges.setStartSeq(0);
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
idwidthAdjuster.setVisible(!wrap);
annotationScroller.setVisible(false);
annotationSpaceFillerHolder.setVisible(false);
}
- else if (av.showAnnotation)
+ else if (av.isShowAnnotation())
{
annotationScroller.setVisible(true);
annotationSpaceFillerHolder.setVisible(true);
+ validateAnnotationDimensions(false);
}
- idSpaceFillerPanel1.setVisible(!wrap);
-
- repaint();
- }
-
- // return value is true if the scroll is valid
- public boolean scrollUp(boolean up)
- {
- if (up)
- {
- if (vscroll.getValue() < 1)
+ int canvasWidth = getSeqPanel().seqCanvas.getWidth();
+ if (canvasWidth > 0)
+ { // may not yet be laid out
+ if (wrap)
{
- return false;
+ int widthInRes = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(canvasWidth);
+ ranges.setViewportWidth(widthInRes);
}
-
- fastPaint = false;
- vscroll.setValue(vscroll.getValue() - 1);
- }
- else
- {
- if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
+ else
{
- return false;
- }
+ int widthInRes = (canvasWidth / av.getCharWidth());
+ int heightInSeq = (getSeqPanel().seqCanvas.getHeight()
+ / av.getCharHeight());
- fastPaint = false;
- vscroll.setValue(vscroll.getValue() + 1);
+ ranges.setViewportWidth(widthInRes);
+ ranges.setViewportHeight(heightInSeq);
+ }
}
- fastPaint = true;
+ idSpaceFillerPanel1.setVisible(!wrap);
- return true;
+ repaint();
}
/**
- * DOCUMENT ME!
+ * Adjust row/column scrollers to show a visible position in the alignment.
*
- * @param right
- * DOCUMENT ME!
+ * @param x
+ * visible column to scroll to
+ * @param y
+ * visible row to scroll to
*
- * @return DOCUMENT ME!
*/
- public boolean scrollRight(boolean right)
+ public void setScrollValues(int xpos, int ypos)
{
- if (!right)
+ int x = xpos;
+ int y = ypos;
+
+ if (av == null || av.getAlignment() == null)
{
- if (hscroll.getValue() < 1)
- {
- return false;
- }
+ return;
+ }
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() - 1);
+ if (av.getWrapAlignment())
+ {
+ setScrollingForWrappedPanel(x);
}
else
{
- if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
+ int width = av.getAlignment().getVisibleWidth();
+ int height = av.getAlignment().getHeight();
+
+ hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+ vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
+
+ if (hextent > width)
{
- return false;
+ hextent = width;
}
- fastPaint = false;
- hscroll.setValue(hscroll.getValue() + 1);
- }
+ if (vextent > height)
+ {
+ vextent = height;
+ }
+
+ if ((hextent + x) > width)
+ {
+ x = width - hextent;
+ }
- fastPaint = true;
+ if ((vextent + y) > height)
+ {
+ y = height - vextent;
+ }
+
+ if (y < 0)
+ {
+ y = 0;
+ }
+
+ if (x < 0)
+ {
+ x = 0;
+ }
- return true;
+ // update the scroll values
+ hscroll.setValues(x, hextent, 0, width);
+ vscroll.setValues(y, vextent, 0, height);
+ }
}
/**
- * Adjust row/column scrollers to show a visible position in the alignment.
+ * Respond to adjustment event when horizontal or vertical scrollbar is
+ * changed
*
- * @param x visible column to scroll to
- * DOCUMENT ME!
- * @param y visible row to scroll to
- *
+ * @param evt
+ * adjustment event encoding whether hscroll or vscroll changed
*/
- public void setScrollValues(int x, int y)
+ @Override
+ public void adjustmentValueChanged(AdjustmentEvent evt)
{
- // System.err.println("Scroll to "+x+","+y);
- if (av == null || av.getAlignment() == null)
+ if (av.getWrapAlignment())
{
+ adjustScrollingWrapped(evt);
return;
}
- int width = av.getAlignment().getWidth();
- int height = av.getAlignment().getHeight();
- if (av.hasHiddenColumns())
- {
- width = av.getColumnSelection().findColumnPosition(width);
- }
-
- av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
-
- hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
- vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
-
- if (hextent > width)
- {
- hextent = width;
- }
+ ViewportRanges ranges = av.getRanges();
- if (vextent > height)
- {
- vextent = height;
- }
-
- if ((hextent + x) > width)
+ if (evt.getSource() == hscroll)
{
- x = width - hextent;
- }
+ int oldX = ranges.getStartRes();
+ int oldwidth = ranges.getViewportWidth();
+ int x = hscroll.getValue();
+ int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
- if ((vextent + y) > height)
- {
- y = height - vextent;
+ // if we're scrolling to the position we're already at, stop
+ // this prevents infinite recursion of events when the scroll/viewport
+ // ranges values are the same
+ if ((x == oldX) && (width == oldwidth))
+ {
+ return;
+ }
+ ranges.setViewportStartAndWidth(x, width);
}
-
- if (y < 0)
+ else if (evt.getSource() == vscroll)
{
- y = 0;
- }
+ int oldY = ranges.getStartSeq();
+ int oldheight = ranges.getViewportHeight();
+ int y = vscroll.getValue();
+ int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
- if (x < 0)
- {
- x = 0;
+ // if we're scrolling to the position we're already at, stop
+ // this prevents infinite recursion of events when the scroll/viewport
+ // ranges values are the same
+ if ((y == oldY) && (height == oldheight))
+ {
+ return;
+ }
+ ranges.setViewportStartAndHeight(y, height);
}
-
- hscroll.setValues(x, hextent, 0, width);
- vscroll.setValues(y, vextent, 0, height);
+ repaint();
}
/**
- * DOCUMENT ME!
+ * Responds to a scroll change by setting the start position of the viewport.
+ * Does
*
* @param evt
- * DOCUMENT ME!
*/
- public void adjustmentValueChanged(AdjustmentEvent evt)
+ protected void adjustScrollingWrapped(AdjustmentEvent evt)
{
-
- int oldX = av.getStartRes();
- int oldY = av.getStartSeq();
-
if (evt.getSource() == hscroll)
{
- int x = hscroll.getValue();
- av.setStartRes(x);
- av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
+ return; // no horizontal scroll when wrapped
}
+ final ViewportRanges ranges = av.getRanges();
if (evt.getSource() == vscroll)
{
- int offy = vscroll.getValue();
+ int newY = vscroll.getValue();
- if (av.getWrapAlignment())
+ /*
+ * if we're scrolling to the position we're already at, stop
+ * this prevents infinite recursion of events when the scroll/viewport
+ * ranges values are the same
+ */
+ int oldX = ranges.getStartRes();
+ int oldY = ranges.getWrappedScrollPosition(oldX);
+ if (oldY == newY)
{
- if (offy > -1)
- {
- int rowSize = seqPanel.seqCanvas
- .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
- av.setStartRes(offy * rowSize);
- av.setEndRes((offy + 1) * rowSize);
- }
- else
- {
- // This is only called if file loaded is a jar file that
- // was wrapped when saved and user has wrap alignment true
- // as preference setting
- SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- setScrollValues(av.getStartRes(), av.getStartSeq());
- }
- });
- }
+ return;
}
- else
+ if (newY > -1)
{
- av.setStartSeq(offy);
- av.setEndSeq(offy
- + (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
+ /*
+ * limit page up/down to one width's worth of positions
+ */
+ int rowSize = ranges.getViewportWidth();
+ int newX = newY > oldY ? oldX + rowSize : oldX - rowSize;
+ ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize);
}
}
-
- if (overviewPanel != null)
- {
- overviewPanel.setBoxPosition();
- }
-
- int scrollX = av.startRes - oldX;
- int scrollY = av.startSeq - oldY;
-
- if (av.getWrapAlignment() || !fastPaint)
- {
- repaint();
- }
else
{
- // Make sure we're not trying to draw a panel
- // larger than the visible window
- if (scrollX > av.endRes - av.startRes)
+ // This is only called if file loaded is a jar file that
+ // was wrapped when saved and user has wrap alignment true
+ // as preference setting
+ SwingUtilities.invokeLater(new Runnable()
{
- scrollX = av.endRes - av.startRes;
- }
- else if (scrollX < av.startRes - av.endRes)
- {
- scrollX = av.startRes - av.endRes;
- }
-
- if (scrollX != 0 || scrollY != 0)
- {
- idPanel.idCanvas.fastPaint(scrollY);
- seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
- scalePanel.repaint();
-
- if (av.getShowAnnotation())
+ @Override
+ public void run()
{
- annotationPanel.fastPaint(scrollX);
+ // When updating scrolling to use ViewportChange events, this code
+ // could not be validated and it is not clear if it is now being
+ // called. Log warning here in case it is called and unforeseen
+ // problems occur
+ Console.warn(
+ "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences");
+
+ // scroll to start of panel
+ ranges.setStartRes(0);
+ ranges.setStartSeq(0);
}
- }
+ });
}
+ repaint();
}
- public void paintAlignment(boolean updateOverview)
+ /* (non-Javadoc)
+ * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean)
+ */
+ @Override
+ public void paintAlignment(boolean updateOverview,
+ boolean updateStructures)
{
+ final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+ av.isShowAutocalculatedAbove());
+ sorter.sort(getAlignment().getAlignmentAnnotation(),
+ av.getSortAnnotationsBy());
repaint();
- if (updateOverview)
+ if (updateStructures)
{
av.getStructureSelectionManager().sequenceColoursChanged(this);
+ }
+ if (updateOverview)
+ {
if (overviewPanel != null)
{
}
}
- /**
- * DOCUMENT ME!
- *
- * @param g
- * DOCUMENT ME!
- */
+ @Override
public void paintComponent(Graphics g)
{
- invalidate();
+ invalidate(); // needed so that the id width adjuster works correctly
- Dimension d = idPanel.idCanvas.getPreferredSize();
+ Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
idPanelHolder.setPreferredSize(d);
hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
- validate();
-
- if (av.getWrapAlignment())
- {
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
- }
+ validate(); // needed so that the id width adjuster works correctly
- int canvasWidth = seqPanel.seqCanvas
- .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
- if (canvasWidth > 0)
- {
- int max = maxwidth
- / seqPanel.seqCanvas
- .getWrappedCanvasWidth(seqPanel.seqCanvas
- .getWidth()) + 1;
- vscroll.setMaximum(max);
- vscroll.setUnitIncrement(1);
- vscroll.setVisibleAmount(1);
- }
- }
- else
- {
- setScrollValues(av.getStartRes(), av.getStartSeq());
- }
+ /*
+ * set scroll bar positions - tried to remove but necessary for split panel to resize correctly
+ * though I still think this call should be elsewhere.
+ */
+ ViewportRanges ranges = av.getRanges();
+ setScrollValues(ranges.getStartRes(), ranges.getStartSeq());
+ super.paintComponent(g);
+ }
+
+ /**
+ * Set vertical scroll bar position, and number of increments, for wrapped
+ * panel
+ *
+ * @param topLeftColumn
+ * the column position at top left (0..)
+ */
+ private void setScrollingForWrappedPanel(int topLeftColumn)
+ {
+ ViewportRanges ranges = av.getRanges();
+ int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn);
+ int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn);
+
+ /*
+ * a scrollbar's value can be set to at most (maximum-extent)
+ * so we add extent (1) to the maxScroll value
+ */
+ vscroll.setUnitIncrement(1);
+ vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1);
}
/**
* @throws PrinterException
* DOCUMENT ME!
*/
+ @Override
public int print(Graphics pg, PageFormat pf, int pi)
throws PrinterException
{
if (av.getWrapAlignment())
{
- return printWrappedAlignment(pg, pwidth, pheight, pi);
+ return printWrappedAlignment(pwidth, pheight, pi, pg);
}
else
{
- return printUnwrapped(pg, pwidth, pheight, pi);
+ return printUnwrapped(pwidth, pheight, pi, pg, pg);
}
}
/**
- * DOCUMENT ME!
- *
- * @param pg
- * DOCUMENT ME!
- * @param pwidth
- * DOCUMENT ME!
- * @param pheight
- * DOCUMENT ME!
- * @param pi
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Draws the alignment image, including sequence ids, sequences, and
+ * annotation labels and annotations if shown, on either one or two Graphics
+ * contexts.
*
+ * @param pageWidth
+ * in pixels
+ * @param pageHeight
+ * in pixels
+ * @param pageIndex
+ * (0, 1, ...)
+ * @param idGraphics
+ * the graphics context for sequence ids and annotation labels
+ * @param alignmentGraphics
+ * the graphics context for sequences and annotations (may or may not
+ * be the same context as idGraphics)
+ * @return
* @throws PrinterException
- * DOCUMENT ME!
*/
- public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
+ public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex,
+ Graphics idGraphics, Graphics alignmentGraphics)
throws PrinterException
{
- int idWidth = getVisibleIdWidth(false);
- FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
-
- pg.setColor(Color.white);
- pg.fillRect(0, 0, pwidth, pheight);
- pg.setFont(av.getFont());
-
- // //////////////////////////////////
- // / How many sequences and residues can we fit on a printable page?
- int totalRes = (pwidth - idWidth) / av.getCharWidth();
+ final int idWidth = getVisibleIdWidth(false);
- int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) - 1;
+ /*
+ * Get the horizontal offset to where we draw the sequences.
+ * This is idWidth if using a single Graphics context, else zero.
+ */
+ final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0
+ : idWidth;
- int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
-
- // ///////////////////////////
- // / Only print these sequences and residues on this page
- int startRes;
+ FontMetrics fm = getFontMetrics(av.getFont());
+ final int charHeight = av.getCharHeight();
+ final int scaleHeight = charHeight + fm.getDescent();
- // ///////////////////////////
- // / Only print these sequences and residues on this page
- int endRes;
+ idGraphics.setColor(Color.white);
+ idGraphics.fillRect(0, 0, pageWidth, pageHeight);
+ idGraphics.setFont(av.getFont());
- // ///////////////////////////
- // / Only print these sequences and residues on this page
- int startSeq;
+ /*
+ * How many sequences and residues can we fit on a printable page?
+ */
+ final int totalRes = (pageWidth - idWidth) / av.getCharWidth();
- // ///////////////////////////
- // / Only print these sequences and residues on this page
- int endSeq;
- startRes = (pi % pagesWide) * totalRes;
- endRes = (startRes + totalRes) - 1;
+ final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1;
- if (endRes > (av.getAlignment().getWidth() - 1))
- {
- endRes = av.getAlignment().getWidth() - 1;
- }
+ final int alignmentWidth = av.getAlignment().getVisibleWidth();
+ int pagesWide = (alignmentWidth / totalRes) + 1;
- startSeq = (pi / pagesWide) * totalSeq;
- endSeq = startSeq + totalSeq;
+ final int startRes = (pageIndex % pagesWide) * totalRes;
+ final int endRes = Math.min(startRes + totalRes - 1,
+ alignmentWidth - 1);
- if (endSeq > av.getAlignment().getHeight())
- {
- endSeq = av.getAlignment().getHeight();
- }
+ final int startSeq = (pageIndex / pagesWide) * totalSeq;
+ final int alignmentHeight = av.getAlignment().getHeight();
+ final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight);
- int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1) * pheight;
+ int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight;
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
- pagesHigh += annotationPanel.adjustPanelHeight() + 3;
+ pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
}
- pagesHigh /= pheight;
+ pagesHigh /= pageHeight;
- if (pi >= (pagesWide * pagesHigh))
+ if (pageIndex >= (pagesWide * pagesHigh))
{
return Printable.NO_SUCH_PAGE;
}
-
- // draw Scale
- pg.translate(idWidth, 0);
- scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth,
- scaleHeight);
- pg.translate(-idWidth, scaleHeight);
-
- // //////////////
- // Draw the ids
- Color currentColor = null;
- Color currentTextColor = null;
-
- pg.setFont(idPanel.idCanvas.idfont);
-
- SequenceI seq;
- for (int i = startSeq; i < endSeq; i++)
- {
- seq = av.getAlignment().getSequenceAt(i);
- if ((av.getSelectionGroup() != null)
- && av.getSelectionGroup().getSequences(null).contains(seq))
- {
- currentColor = Color.gray;
- currentTextColor = Color.black;
- }
- else
- {
- currentColor = av.getSequenceColour(seq);
- currentTextColor = Color.black;
- }
-
- pg.setColor(currentColor);
- pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
- av.getCharHeight());
-
- pg.setColor(currentTextColor);
-
- int xPos = 0;
- if (av.rightAlignIds)
- {
- fm = pg.getFontMetrics();
- xPos = idWidth
- - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix()))
- - 4;
- }
-
- pg.drawString(
- seq.getDisplayId(av.getShowJVSuffix()),
- xPos,
- (((i - startSeq) * av.charHeight) + av.getCharHeight())
- - (av.getCharHeight() / 5));
- }
-
- pg.setFont(av.getFont());
-
- // draw main sequence panel
- pg.translate(idWidth, 0);
- seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
-
- if (av.showAnnotation && (endSeq == av.getAlignment().getHeight()))
- {
- pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
- alabels.drawComponent((Graphics2D) pg, idWidth);
- pg.translate(idWidth + 3, 0);
- annotationPanel.renderer.drawComponent(annotationPanel, av, (Graphics2D) pg, -1, startRes, endRes + 1);
+ final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
+
+ /*
+ * draw the Scale at horizontal offset, then reset to top left (0, 0)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset, 0);
+ getScalePanel().drawScale(alignmentGraphics, startRes, endRes,
+ pageWidth - idWidth, scaleHeight);
+ alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
+
+ /*
+ * Draw the sequence ids, offset for scale height,
+ * then reset to top left (0, 0)
+ */
+ idGraphics.translate(0, scaleHeight);
+ IdCanvas idCanvas = getIdPanel().getIdCanvas();
+ List<SequenceI> selection = av.getSelectionGroup() == null ? null
+ : av.getSelectionGroup().getSequences(null);
+ idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
+ selection);
+
+ idGraphics.setFont(av.getFont());
+ idGraphics.translate(0, -scaleHeight);
+
+ /*
+ * draw the sequences, offset for scale height, and id width (if using a
+ * single graphics context), then reset to (0, scale height)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight);
+ getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes,
+ endRes, startSeq, endSeq - 1);
+ alignmentGraphics.translate(-alignmentGraphicsOffset, 0);
+
+ if (av.isShowAnnotation() && (endSeq == alignmentHeight))
+ {
+ /*
+ * draw annotation labels; drawComponent() translates by
+ * getScrollOffset(), so compensate for that first;
+ * then reset to (0, scale height)
+ */
+ int offset = getAlabels().getScrollOffset();
+ idGraphics.translate(0, -offset);
+ idGraphics.translate(0, alignmentDrawnHeight);
+ getAlabels().drawComponent(idGraphics, idWidth);
+ idGraphics.translate(0, -alignmentDrawnHeight);
+
+ /*
+ * draw the annotations starting at
+ * (idOffset, alignmentHeight) from (0, scaleHeight)
+ */
+ alignmentGraphics.translate(alignmentGraphicsOffset,
+ alignmentDrawnHeight);
+ getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
+ alignmentGraphics, -1, startRes, endRes + 1);
}
return Printable.PAGE_EXISTS;
}
/**
- * DOCUMENT ME!
+ * Prints one page of an alignment in wrapped mode. Returns
+ * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if
+ * no page could be drawn (page number out of range).
*
- * @param pg
- * DOCUMENT ME!
- * @param pwidth
- * DOCUMENT ME!
- * @param pheight
- * DOCUMENT ME!
- * @param pi
- * DOCUMENT ME!
+ * @param pageWidth
+ * @param pageHeight
+ * @param pageNumber
+ * (0, 1, ...)
+ * @param g
*
- * @return DOCUMENT ME!
+ * @return
*
* @throws PrinterException
- * DOCUMENT ME!
*/
- public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
- int pi) throws PrinterException
+ public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber,
+ Graphics g) throws PrinterException
{
-
+ getSeqPanel().seqCanvas.calculateWrappedGeometry(getWidth(),
+ getHeight());
int annotationHeight = 0;
- AnnotationLabels labels = null;
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
- annotationHeight = annotationPanel.adjustPanelHeight();
- labels = new AnnotationLabels(av);
+ annotationHeight = getAnnotationPanel().adjustPanelHeight();
}
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
+ annotationHeight;
int idWidth = getVisibleIdWidth(false);
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
- }
+ int maxwidth = av.getAlignment().getVisibleWidth();
- int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth
- - idWidth);
+ int resWidth = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(pageWidth - idWidth);
+ av.getRanges().setViewportStartAndWidth(0, resWidth);
int totalHeight = cHeight * (maxwidth / resWidth + 1);
- pg.setColor(Color.white);
- pg.fillRect(0, 0, pwidth, pheight);
- pg.setFont(av.getFont());
+ g.setColor(Color.white);
+ g.fillRect(0, 0, pageWidth, pageHeight);
+ g.setFont(av.getFont());
+ g.setColor(Color.black);
- // //////////////
- // Draw the ids
- pg.setColor(Color.black);
+ /*
+ * method: print the whole wrapped alignment, but with a clip region that
+ * is restricted to the requested page; this supports selective print of
+ * single pages or ranges, (at the cost of repeated processing in the
+ * 'normal' case, when all pages are printed)
+ */
+ g.translate(0, -pageNumber * pageHeight);
- pg.translate(0, -pi * pheight);
+ g.setClip(0, pageNumber * pageHeight, pageWidth, pageHeight);
- pg.setClip(0, pi * pheight, pwidth, pheight);
+ /*
+ * draw sequence ids and annotation labels (if shown)
+ */
+ IdCanvas idCanvas = getIdPanel().getIdCanvas();
+ idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight);
- int ypos = hgap;
+ g.translate(idWidth, 0);
- do
- {
- for (int i = 0; i < av.getAlignment().getHeight(); i++)
- {
- pg.setFont(idPanel.idCanvas.idfont);
- SequenceI s = av.getAlignment().getSequenceAt(i);
- String string = s.getDisplayId(av.getShowJVSuffix());
- int xPos = 0;
- if (av.rightAlignIds)
- {
- FontMetrics fm = pg.getFontMetrics();
- xPos = idWidth - fm.stringWidth(string) - 4;
- }
- pg.drawString(string, xPos,
- ((i * av.charHeight) + ypos + av.charHeight)
- - (av.charHeight / 5));
- }
- if (labels != null)
- {
- pg.translate(-3, ypos
- + (av.getAlignment().getHeight() * av.charHeight));
-
- pg.setFont(av.getFont());
- labels.drawComponent(pg, idWidth);
- pg.translate(+3, -ypos
- - (av.getAlignment().getHeight() * av.charHeight));
- }
+ getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth,
+ totalHeight, 0);
- ypos += cHeight;
- } while (ypos < totalHeight);
-
- pg.translate(idWidth, 0);
-
- seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
- 0);
-
- if ((pi * pheight) < totalHeight)
+ if ((pageNumber * pageHeight) < totalHeight)
{
return Printable.PAGE_EXISTS;
-
}
else
{
return Printable.NO_SUCH_PAGE;
}
}
+
/**
- * get current sequence ID panel width, or nominal value if panel were to be displayed using default settings
+ * get current sequence ID panel width, or nominal value if panel were to be
+ * displayed using default settings
+ *
* @return
*/
- int getVisibleIdWidth()
+ public int getVisibleIdWidth()
{
return getVisibleIdWidth(true);
}
/**
- * get current sequence ID panel width, or nominal value if panel were to be displayed using default settings
- * @param onscreen indicate if the Id width for onscreen or offscreen display should be returned
+ * get current sequence ID panel width, or nominal value if panel were to be
+ * displayed using default settings
+ *
+ * @param onscreen
+ * indicate if the Id width for onscreen or offscreen display should
+ * be returned
* @return
*/
- int getVisibleIdWidth(boolean onscreen)
+ protected int getVisibleIdWidth(boolean onscreen)
{
// see if rendering offscreen - check preferences and calc width accordingly
if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
{
- return calculateIdWidth(-1).width+4;
+ return calculateIdWidth(-1).width;
}
- Integer idwidth=null;
- if (onscreen || (idwidth=Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"))==null) {
- return (idPanel.getWidth() > 0 ? idPanel.getWidth()
- : calculateIdWidth().width + 4);
+ Integer idwidth = onscreen ? null
+ : Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
+ if (idwidth != null)
+ {
+ return idwidth.intValue() + ID_WIDTH_PADDING;
}
- return idwidth.intValue()+4;
+
+ int w = getIdPanel().getWidth();
+ return (w > 0 ? w : calculateIdWidth().width);
}
- void makeAlignmentImage(int type, File file)
+ /**
+ * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and
+ * writes it to the specified file
+ *
+ * @param type
+ * @param file
+ */
+ void makeAlignmentImage(ImageMaker.TYPE type, File file)
{
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
+ final int borderBottomOffset = 5;
+
+ AlignmentDimension aDimension = getAlignmentDimension();
+ // todo use a lambda function in place of callback here?
+ ImageWriterI writer = new ImageWriterI()
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
- }
+ @Override
+ public void exportImage(Graphics graphics) throws Exception
+ {
+ if (av.getWrapAlignment())
+ {
+ printWrappedAlignment(aDimension.getWidth(),
+ aDimension.getHeight() + borderBottomOffset, 0, graphics);
+ }
+ else
+ {
+ printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0,
+ graphics, graphics);
+ }
+ }
+ };
+
+ String fileTitle = alignFrame.getTitle();
+ ImageExporter exporter = new ImageExporter(writer, alignFrame, type,
+ fileTitle);
+ int imageWidth = aDimension.getWidth();
+ int imageHeight = aDimension.getHeight() + borderBottomOffset;
+ String of = MessageManager.getString("label.alignment");
+ exporter.doExport(file, this, imageWidth, imageHeight, of);
+ }
- int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
- + scalePanel.getHeight();
- int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth);
+ /**
+ * Calculates and returns a suitable width and height (in pixels) for an
+ * exported image
+ *
+ * @return
+ */
+ public AlignmentDimension getAlignmentDimension()
+ {
+ int maxwidth = av.getAlignment().getVisibleWidth();
+
+ int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight())
+ + getScalePanel().getHeight();
+ int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
if (av.getWrapAlignment())
{
height = getWrappedHeight();
- if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
+ if (Jalview.isHeadlessMode())
{
- // need to obtain default alignment width and then add in any additional allowance for id margin
- // this duplicates the calculation in getWrappedHeight but adjusts for offscreen idWith
+ // need to obtain default alignment width and then add in any
+ // additional allowance for id margin
+ // this duplicates the calculation in getWrappedHeight but adjusts for
+ // offscreen idWith
width = alignFrame.getWidth() - vscroll.getPreferredSize().width
- - alignFrame.getInsets().left
- - alignFrame.getInsets().right
- - getVisibleIdWidth()+getVisibleIdWidth(false);
+ - alignFrame.getInsets().left - alignFrame.getInsets().right
+ - getVisibleIdWidth() + getVisibleIdWidth(false);
}
else
{
- width = seqPanel.getWidth() + getVisibleIdWidth(false);
+ width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
}
}
- else if (av.getShowAnnotation())
+ else if (av.isShowAnnotation())
{
- height += annotationPanel.adjustPanelHeight() + 3;
+ height += getAnnotationPanel().adjustPanelHeight() + 3;
}
+ return new AlignmentDimension(width, height);
- try
- {
-
- jalview.util.ImageMaker im;
- if (type == jalview.util.ImageMaker.PNG)
- {
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG,
- "Create PNG image from alignment", width, height, file,
- null);
- }
- else
- {
- im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
- "Create EPS file from alignment", width, height, file,
- alignFrame.getTitle());
- }
-
- if (av.getWrapAlignment())
- {
- if (im.getGraphics() != null)
- {
- printWrappedAlignment(im.getGraphics(), width, height, 0);
- im.writeImage();
- }
- }
- else
- {
- if (im.getGraphics() != null)
- {
- printUnwrapped(im.getGraphics(), width, height, 0);
- im.writeImage();
- }
- }
- } catch (OutOfMemoryError err)
- {
- // Be noisy here.
- System.out.println("########################\n" + "OUT OF MEMORY "
- + file + "\n" + "########################");
- new OOMWarning("Creating Image for " + file, err);
- // System.out.println("Create IMAGE: " + err);
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- /**
- * DOCUMENT ME!
- */
- public void makeEPS(File epsFile)
- {
- makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
- }
-
- /**
- * DOCUMENT ME!
- */
- public void makePNG(File pngFile)
- {
- makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
}
public void makePNGImageMap(File imgMapFile, String imageName)
{
- // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+ // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
// ////////////////////////////////////////////
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
+ int scaleHeight = av.getCharHeight() + fm.getDescent();
// Gen image map
// ////////////////////////////////
{
try
{
- int s, sSize = av.getAlignment().getHeight(), res, alwidth = av.getAlignment()
- .getWidth(), g, gSize, f, fSize, sy;
- StringBuffer text = new StringBuffer();
+ int sSize = av.getAlignment().getHeight();
+ int alwidth = av.getAlignment().getWidth();
PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
- out.println(jalview.io.HTMLOutput.getImageMapHTML());
+ out.println(HTMLOutput.getImageMapHTML());
out.println("<img src=\"" + imageName
+ "\" border=\"0\" usemap=\"#Map\" >"
+ "<map name=\"Map\">");
- for (s = 0; s < sSize; s++)
+ for (int s = 0; s < sSize; s++)
{
- sy = s * av.charHeight + scaleHeight;
+ int sy = s * av.getCharHeight() + scaleHeight;
SequenceI seq = av.getAlignment().getSequenceAt(s);
- SequenceFeature[] features = seq.getDatasetSequence()
- .getSequenceFeatures();
SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
- for (res = 0; res < alwidth; res++)
+ for (int column = 0; column < alwidth; column++)
{
- text = new StringBuffer();
- Object obj = null;
+ StringBuilder text = new StringBuilder(512);
+ String triplet = null;
if (av.getAlignment().isNucleotide())
{
- obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
- + "");
+ triplet = ResidueProperties.nucleotideName.get(seq
+ .getCharAt(column) + "");
}
else
{
- obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+ triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column)
+ "");
}
- if (obj == null)
+ if (triplet == null)
{
continue;
}
- String triplet = obj.toString();
- int alIndex = seq.findPosition(res);
- gSize = groups.length;
- for (g = 0; g < gSize; g++)
+ int seqPos = seq.findPosition(column);
+ int gSize = groups.length;
+ for (int g = 0; g < gSize; g++)
{
if (text.length() < 1)
{
- text.append("<area shape=\"rect\" coords=\""
- + (idWidth + res * av.charWidth) + "," + sy + ","
- + (idWidth + (res + 1) * av.charWidth) + ","
- + (av.charHeight + sy) + "\""
- + " onMouseOver=\"toolTip('" + alIndex + " "
- + triplet);
+ text.append("<area shape=\"rect\" coords=\"")
+ .append((idWidth + column * av.getCharWidth()))
+ .append(",").append(sy).append(",")
+ .append((idWidth + (column + 1) * av.getCharWidth()))
+ .append(",").append((av.getCharHeight() + sy))
+ .append("\"").append(" onMouseOver=\"toolTip('")
+ .append(seqPos).append(" ").append(triplet);
}
- if (groups[g].getStartRes() < res
- && groups[g].getEndRes() > res)
+ if (groups[g].getStartRes() < column
+ && groups[g].getEndRes() > column)
{
- text.append("<br><em>" + groups[g].getName() + "</em>");
+ text.append("<br><em>").append(groups[g].getName())
+ .append("</em>");
}
}
- if (features != null)
+ if (text.length() < 1)
{
- if (text.length() < 1)
- {
- text.append("<area shape=\"rect\" coords=\""
- + (idWidth + res * av.charWidth) + "," + sy + ","
- + (idWidth + (res + 1) * av.charWidth) + ","
- + (av.charHeight + sy) + "\""
- + " onMouseOver=\"toolTip('" + alIndex + " "
- + triplet);
- }
- fSize = features.length;
- for (f = 0; f < fSize; f++)
+ text.append("<area shape=\"rect\" coords=\"")
+ .append((idWidth + column * av.getCharWidth()))
+ .append(",").append(sy).append(",")
+ .append((idWidth + (column + 1) * av.getCharWidth()))
+ .append(",").append((av.getCharHeight() + sy))
+ .append("\"").append(" onMouseOver=\"toolTip('")
+ .append(seqPos).append(" ").append(triplet);
+ }
+ if (!Comparison.isGap(seq.getCharAt(column)))
+ {
+ List<SequenceFeature> features = seq.findFeatures(column, column);
+ for (SequenceFeature sf : features)
{
-
- if ((features[f].getBegin() <= seq.findPosition(res))
- && (features[f].getEnd() >= seq.findPosition(res)))
+ if (sf.isContactFeature())
{
- if (features[f].getType().equals("disulfide bond"))
- {
- if (features[f].getBegin() == seq.findPosition(res)
- || features[f].getEnd() == seq
- .findPosition(res))
- {
- text.append("<br>disulfide bond "
- + features[f].getBegin() + ":"
- + features[f].getEnd());
- }
- }
- else
+ text.append("<br>").append(sf.getType()).append(" ")
+ .append(sf.getBegin()).append(":")
+ .append(sf.getEnd());
+ }
+ else
+ {
+ text.append("<br>");
+ text.append(sf.getType());
+ String description = sf.getDescription();
+ if (description != null
+ && !sf.getType().equals(description))
{
- text.append("<br>");
- text.append(features[f].getType());
- if (features[f].getDescription() != null
- && !features[f].getType().equals(
- features[f].getDescription()))
- {
- text.append(" " + features[f].getDescription());
- }
-
- if (features[f].getValue("status") != null)
- {
- text.append(" (" + features[f].getValue("status")
- + ")");
- }
+ description = description.replace("\"", """);
+ text.append(" ").append(description);
}
}
-
+ String status = sf.getStatus();
+ if (status != null && !"".equals(status))
+ {
+ text.append(" (").append(status).append(")");
+ }
+ }
+ if (text.length() > 1)
+ {
+ text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
+ out.println(text.toString());
}
- }
- if (text.length() > 1)
- {
- text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">");
- out.println(text.toString());
}
}
}
}
+ /**
+ * Answers the height of the entire alignment in pixels, assuming it is in
+ * wrapped mode
+ *
+ * @return
+ */
int getWrappedHeight()
{
- int seqPanelWidth = seqPanel.seqCanvas.getWidth();
+ int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
if (System.getProperty("java.awt.headless") != null
&& System.getProperty("java.awt.headless").equals("true"))
- alignFrame.getInsets().left - alignFrame.getInsets().right;
}
- int chunkWidth = seqPanel.seqCanvas
+ int chunkWidth = getSeqPanel().seqCanvas
.getWrappedCanvasWidth(seqPanelWidth);
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
+ int hgap = av.getCharHeight();
+ if (av.getScaleAboveWrapped())
{
- hgap += av.charHeight;
+ hgap += av.getCharHeight();
}
int annotationHeight = 0;
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
- annotationHeight = annotationPanel.adjustPanelHeight();
+ hgap += SeqCanvas.SEQS_ANNOTATION_GAP;
+ annotationHeight = getAnnotationPanel().adjustPanelHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap
+ annotationHeight;
int maxwidth = av.getAlignment().getWidth();
if (av.hasHiddenColumns())
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
+ maxwidth = av.getAlignment().getHiddenColumns()
+ .absoluteToVisibleColumn(maxwidth) - 1;
}
int height = ((maxwidth / chunkWidth) + 1) * cHeight;
*/
public void closePanel()
{
- PaintRefresher.RemoveComponent(seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(idPanel.idCanvas);
+ PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
+ PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
PaintRefresher.RemoveComponent(this);
+
+ closeChildFrames();
+
+ /*
+ * try to ensure references are nulled
+ */
+ if (annotationPanel != null)
+ {
+ annotationPanel.dispose();
+ annotationPanel = null;
+ }
+
if (av != null)
{
- jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager();
- ssm.removeStructureViewerListener(seqPanel, null);
- ssm.removeSelectionListener(seqPanel);
- av.setAlignment(null);
+ av.removePropertyChangeListener(propertyChangeListener);
+ propertyChangeListener = null;
+ StructureSelectionManager ssm = av.getStructureSelectionManager();
+ ssm.removeStructureViewerListener(getSeqPanel(), null);
+ ssm.removeSelectionListener(getSeqPanel());
+ ssm.removeCommandListener(av);
+ ssm.removeStructureViewerListener(getSeqPanel(), null);
+ ssm.removeSelectionListener(getSeqPanel());
+ av.dispose();
av = null;
}
else
{
- if (Cache.log.isDebugEnabled())
+ if (Console.isDebugEnabled())
{
- Cache.log.warn("Closing alignment panel which is already closed.");
+ Console.warn("Closing alignment panel which is already closed.");
}
}
}
/**
+ * Close any open dialogs that would be orphaned when this one is closed
+ */
+ protected void closeChildFrames()
+ {
+ if (overviewPanel != null)
+ {
+ overviewPanel.dispose();
+ overviewPanel = null;
+ }
+ if (calculationDialog != null)
+ {
+ calculationDialog.closeFrame();
+ calculationDialog = null;
+ }
+ }
+
+ /**
* hides or shows dynamic annotation rows based on groups and av state flags
*/
public void updateAnnotation()
{
- updateAnnotation(false);
+ updateAnnotation(false, false);
}
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();
- boolean normLogo = av.isNormaliseSequenceLogo();
+ 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 == null ? null : av.getAlignment();
+ }
- // intersect alignment annotation with alignment groups
+ @Override
+ public String getViewName()
+ {
+ return av.getViewName();
+ }
- AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation();
- Hashtable oldrfs = new Hashtable();
- if (aan != null)
+ /**
+ * Make/Unmake this alignment panel the current input focus
+ *
+ * @param b
+ */
+ public void setSelected(boolean b)
+ {
+ try
{
- for (int an = 0; an < aan.length; an++)
+ if (alignFrame.getSplitViewContainer() != null)
{
- if (aan[an].autoCalculated && aan[an].groupRef != null)
- {
- oldrfs.put(aan[an].groupRef, aan[an].groupRef);
- av.getAlignment().deleteAnnotation(aan[an]);
- aan[an] = null;
- }
+ /*
+ * bring enclosing SplitFrame to front first if there is one
+ */
+ ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b);
}
+ alignFrame.setSelected(b);
+ } catch (Exception ex)
+ {
}
- if (av.getAlignment().getGroups()!=null)
+ if (b)
{
- for (SequenceGroup sg:av.getAlignment().getGroups())
- {
- updateCalcs = false;
- if (applyGlobalSettings || !oldrfs.containsKey(sg))
- {
- // set defaults for this group's conservation/consensus
- sg.setshowSequenceLogo(showprf);
- sg.setShowConsensusHistogram(showConsHist);
- sg.setNormaliseSequenceLogo(normLogo);
- }
- if (conv)
- {
- updateCalcs = true;
- av.getAlignment().addAnnotation(sg.getConservationRow(), 0);
- }
- if (cons)
- {
- updateCalcs = true;
- av.getAlignment().addAnnotation(sg.getConsensus(), 0);
- }
- // refresh the annotation rows
- if (updateCalcs)
- {
- sg.recalcConservation();
- }
- }
+ setAlignFrameView();
}
- oldrfs.clear();
- adjustAnnotationHeight();
+ }
+ public void setAlignFrameView()
+ {
+ alignFrame.setDisplayedView(this);
+ }
+
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return av.getStructureSelectionManager();
}
@Override
- public AlignmentI getAlignment()
+ public void raiseOOMWarning(String string, OutOfMemoryError error)
+ {
+ new OOMWarning(string, error, this);
+ }
+
+ @Override
+ public jalview.api.FeatureRenderer cloneFeatureRenderer()
+ {
+
+ return new FeatureRenderer(this);
+ }
+
+ @Override
+ public jalview.api.FeatureRenderer getFeatureRenderer()
+ {
+ return seqPanel.seqCanvas.getFeatureRenderer();
+ }
+
+ public void updateFeatureRenderer(
+ jalview.renderer.seqfeatures.FeatureRenderer fr)
+ {
+ fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
+ }
+
+ public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
+ {
+ if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
+ {
+ getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
+ }
+ }
+
+ public ScalePanel getScalePanel()
+ {
+ return scalePanel;
+ }
+
+ public void setScalePanel(ScalePanel scalePanel)
+ {
+ this.scalePanel = scalePanel;
+ }
+
+ public SeqPanel getSeqPanel()
{
- return av.getAlignment();
+ return seqPanel;
+ }
+
+ public void setSeqPanel(SeqPanel seqPanel)
+ {
+ this.seqPanel = seqPanel;
+ }
+
+ public AnnotationPanel getAnnotationPanel()
+ {
+ return annotationPanel;
+ }
+
+ public void setAnnotationPanel(AnnotationPanel annotationPanel)
+ {
+ this.annotationPanel = annotationPanel;
+ }
+
+ public AnnotationLabels getAlabels()
+ {
+ return alabels;
+ }
+
+ public void setAlabels(AnnotationLabels alabels)
+ {
+ this.alabels = alabels;
+ }
+
+ public IdPanel getIdPanel()
+ {
+ return idPanel;
+ }
+
+ public void setIdPanel(IdPanel idPanel)
+ {
+ this.idPanel = idPanel;
}
/**
- * get the name for this view
- * @return
+ * 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 verticalOffset
+ * the number of visible sequences to show above the mapped region
*/
- public String getViewName()
+ protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
{
- return av.viewName;
+ scrollToPosition(sr, verticalOffset, true);
}
/**
- * Make/Unmake this alignment panel the current input focus
+ * Set a flag to say do not scroll any (cDNA/protein) complement.
+ *
* @param b
*/
- public void setSelected(boolean b)
+ protected void setToScrollComplementPanel(boolean b)
{
- try {
- alignFrame.setSelected(b);
- } catch (Exception ex) {};
-
- if (b)
+ this.scrollComplementaryPanel = b;
+ }
+
+ /**
+ * Get whether to scroll complement panel
+ *
+ * @return true if cDNA/protein complement panels should be scrolled
+ */
+ protected boolean isSetToScrollComplementPanel()
+ {
+ return this.scrollComplementaryPanel;
+ }
+
+ /**
+ * Redraw sensibly.
+ *
+ * @adjustHeight if true, try to recalculate panel height for visible
+ * annotations
+ */
+ protected void refresh(boolean adjustHeight)
+ {
+ validateAnnotationDimensions(adjustHeight);
+ addNotify();
+ if (adjustHeight)
+ {
+ // sort, repaint, update overview
+ paintAlignment(true, false);
+ }
+ else
{
- alignFrame.setDisplayedView(this);
- }
+ // lightweight repaint
+ repaint();
+ }
}
@Override
- public StructureSelectionManager getStructureSelectionManager()
+ /**
+ * Property change event fired when a change is made to the viewport ranges
+ * object associated with this alignment panel's viewport
+ */
+ public void propertyChange(PropertyChangeEvent evt)
{
- return av.getStructureSelectionManager();
+ // update this panel's scroll values based on the new viewport ranges values
+ ViewportRanges ranges = av.getRanges();
+ int x = ranges.getStartRes();
+ int y = ranges.getStartSeq();
+ setScrollValues(x, y);
+
+ // now update any complementary alignment (its viewport ranges object
+ // is different so does not get automatically updated)
+ if (isSetToScrollComplementPanel())
+ {
+ setToScrollComplementPanel(false);
+ av.scrollComplementaryAlignment();
+ setToScrollComplementPanel(true);
+ }
}
- @Override
- public void raiseOOMWarning(String string, OutOfMemoryError error)
+ /**
+ * Set the reference to the PCA/Tree chooser dialog for this panel. This
+ * reference should be nulled when the dialog is closed.
+ *
+ * @param calculationChooser
+ */
+ public void setCalculationDialog(CalculationChooser calculationChooser)
{
- new OOMWarning(string, error, this);
+ calculationDialog = calculationChooser;
}
+
+ /**
+ * Returns the reference to the PCA/Tree chooser dialog for this panel (null
+ * if none is open)
+ */
+ public CalculationChooser getCalculationDialog()
+ {
+ return calculationDialog;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff