/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
-import java.beans.*;
-import java.io.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import java.awt.print.*;
-import javax.swing.*;
-
+import jalview.analysis.AnnotationSorter;
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
-import jalview.datamodel.*;
-import jalview.jbgui.*;
-import jalview.schemes.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GAlignmentPanel;
+import jalview.math.AlignmentDimension;
+import jalview.schemes.ResidueProperties;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+
+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.event.AdjustmentEvent;
+import java.awt.event.AdjustmentListener;
+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 javax.swing.SwingUtilities;
/**
* DOCUMENT ME!
OverviewPanel overviewPanel;
- SeqPanel seqPanel;
+ private SeqPanel seqPanel;
- IdPanel idPanel;
+ private IdPanel idPanel;
+ private boolean headless;
IdwidthAdjuster idwidthAdjuster;
/** DOCUMENT ME!! */
public AlignFrame alignFrame;
- ScalePanel scalePanel;
+ private ScalePanel scalePanel;
- AnnotationPanel annotationPanel;
+ private AnnotationPanel annotationPanel;
- AnnotationLabels alabels;
+ private AnnotationLabels alabels;
// this value is set false when selection area being dragged
boolean fastPaint = true;
{
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());
+ setAnnotationVisible(av.isShowAnnotation());
hscroll.addAdjustmentListener(this);
vscroll.addAdjustmentListener(this);
idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight
+ fm.getDescent()));
- idPanel.idCanvas.gg = null;
- seqPanel.seqCanvas.img = null;
- annotationPanel.adjustPanelHeight();
+ 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)
int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
int maxwidth = Math.max(20,
- Math.min(afwidth - 200, (int) 2 * afwidth / 3));
+ Math.min(afwidth - 200, 2 * afwidth / 3));
return calculateIdWidth(maxwidth);
}
if (al.getAlignmentAnnotation() != null)
{
- fm = c.getFontMetrics(alabels.getFont());
+ fm = c.getFontMetrics(getAlabels().getFont());
while (i < al.getAlignmentAnnotation().length)
{
public void highlightSearchResults(SearchResults results)
{
scrollToPosition(results);
- seqPanel.seqCanvas.highlightSearchResults(results);
+ getSeqPanel().seqCanvas.highlightSearchResults(results);
}
/**
void scrollToWrappedVisible(int res)
{
- int cwidth = seqPanel.seqCanvas
- .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+ int cwidth = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
{
vscroll.setValue((res / cwidth));
*/
protected void validateAnnotationDimensions(boolean adjustPanelHeight)
{
- int height = annotationPanel.adjustPanelHeight();
+ int height = getAnnotationPanel().adjustPanelHeight();
int theight = av.getCharHeight()
* (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0
annotationScroller.setVisible(false);
annotationSpaceFillerHolder.setVisible(false);
}
- else if (av.showAnnotation)
+ else if (av.isShowAnnotation())
{
annotationScroller.setVisible(true);
annotationSpaceFillerHolder.setVisible(true);
width = av.getColumnSelection().findColumnPosition(width);
}
- av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
+ av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.charWidth)) - 1);
- hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
- vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
+ hextent = getSeqPanel().seqCanvas.getWidth() / av.charWidth;
+ vextent = getSeqPanel().seqCanvas.getHeight() / av.charHeight;
if (hextent > width)
{
{
int x = hscroll.getValue();
av.setStartRes(x);
- av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
+ av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1);
}
if (evt.getSource() == vscroll)
{
if (offy > -1)
{
- int rowSize = seqPanel.seqCanvas
- .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+ int rowSize = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
av.setStartRes(offy * rowSize);
av.setEndRes((offy + 1) * rowSize);
}
{
av.setStartSeq(offy);
av.setEndSeq(offy
- + (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
+ + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()));
}
}
if (scrollX != 0 || scrollY != 0)
{
- idPanel.idCanvas.fastPaint(scrollY);
- seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
- scalePanel.repaint();
+ getIdPanel().getIdCanvas().fastPaint(scrollY);
+ getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY);
+ getScalePanel().repaint();
- if (av.getShowAnnotation() && scrollX != 0)
+ if (av.isShowAnnotation() && scrollX != 0)
{
- annotationPanel.fastPaint(scrollX);
+ getAnnotationPanel().fastPaint(scrollX);
}
}
}
}
+ /**
+ * Repaint the alignment including the annotations and overview panels (if
+ * shown).
+ */
public void paintAlignment(boolean updateOverview)
{
+ final AnnotationSorter sorter = new AnnotationSorter(getAlignment(),
+ av.isShowAutocalculatedAbove());
+ sorter.sort(getAlignment()
+ .getAlignmentAnnotation(),
+ av.getSortAnnotationsBy());
repaint();
if (updateOverview)
{
invalidate();
- Dimension d = idPanel.idCanvas.getPreferredSize();
+ Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
idPanelHolder.setPreferredSize(d);
hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
validate();
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
- int canvasWidth = seqPanel.seqCanvas
- .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+ int canvasWidth = getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth());
if (canvasWidth > 0)
{
int max = maxwidth
- / seqPanel.seqCanvas
- .getWrappedCanvasWidth(seqPanel.seqCanvas
+ / getSeqPanel().seqCanvas
+ .getWrappedCanvasWidth(getSeqPanel().seqCanvas
.getWidth()) + 1;
vscroll.setMaximum(max);
vscroll.setUnitIncrement(1);
// / How many sequences and residues can we fit on a printable page?
int totalRes = (pwidth - idWidth) / av.getCharWidth();
- int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) - 1;
+ int totalSeq = (pheight - scaleHeight) / av.getCharHeight() - 1;
int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1)
* pheight;
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
- pagesHigh += annotationPanel.adjustPanelHeight() + 3;
+ pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
}
pagesHigh /= pheight;
// draw Scale
pg.translate(idWidth, 0);
- scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth,
+ getScalePanel().drawScale(pg, startRes, endRes, pwidth - idWidth,
scaleHeight);
pg.translate(-idWidth, scaleHeight);
Color currentColor = null;
Color currentTextColor = null;
- pg.setFont(idPanel.idCanvas.idfont);
+ pg.setFont(getIdPanel().getIdCanvas().getIdfont());
SequenceI seq;
for (int i = startSeq; i < endSeq; i++)
pg.setColor(currentTextColor);
int xPos = 0;
- if (av.rightAlignIds)
+ if (av.isRightAlignIds())
{
fm = pg.getFontMetrics();
xPos = idWidth
// draw main sequence panel
pg.translate(idWidth, 0);
- seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
+ getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
- if (av.showAnnotation && (endSeq == av.getAlignment().getHeight()))
+ if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight()))
{
// draw annotation - need to offset for current scroll position
- int offset = -alabels.scrollOffset;
+ int offset = -getAlabels().getScrollOffset();
pg.translate(0, offset);
pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
- alabels.drawComponent((Graphics2D) pg, idWidth);
+ getAlabels().drawComponent(pg, idWidth);
pg.translate(idWidth + 3, 0);
- annotationPanel.renderer.drawComponent(annotationPanel, av,
- (Graphics2D) pg, -1, startRes, endRes + 1);
+ getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av,
+ pg, -1, startRes, endRes + 1);
pg.translate(0, -offset);
}
int annotationHeight = 0;
AnnotationLabels labels = null;
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
- annotationHeight = annotationPanel.adjustPanelHeight();
+ annotationHeight = getAnnotationPanel().adjustPanelHeight();
labels = new AnnotationLabels(av);
}
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
- int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth
+ int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth
- idWidth);
int totalHeight = cHeight * (maxwidth / resWidth + 1);
{
for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
- pg.setFont(idPanel.idCanvas.idfont);
+ pg.setFont(getIdPanel().getIdCanvas().getIdfont());
SequenceI s = av.getAlignment().getSequenceAt(i);
String string = s.getDisplayId(av.getShowJVSuffix());
int xPos = 0;
- if (av.rightAlignIds)
+ if (av.isRightAlignIds())
{
FontMetrics fm = pg.getFontMetrics();
xPos = idWidth - fm.stringWidth(string) - 4;
pg.translate(idWidth, 0);
- seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
+ getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
0);
if ((pi * pheight) < totalHeight)
*
* @return
*/
- int getVisibleIdWidth()
+ public int getVisibleIdWidth()
{
return getVisibleIdWidth(true);
}
* be returned
* @return
*/
- int getVisibleIdWidth(boolean onscreen)
+ public int getVisibleIdWidth(boolean onscreen)
{
// see if rendering offscreen - check preferences and calc width accordingly
if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
if (onscreen
|| (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
{
- return (idPanel.getWidth() > 0 ? idPanel.getWidth()
+ return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth()
: calculateIdWidth().width + 4);
}
return idwidth.intValue() + 4;
}
- void makeAlignmentImage(int type, File file)
+ void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file)
{
long progress = System.currentTimeMillis();
- boolean headless = (System.getProperty("java.awt.headless") != null && System
+ headless = (System.getProperty("java.awt.headless") != null && System
.getProperty("java.awt.headless").equals("true"));
if (alignFrame != null && !headless)
{
- alignFrame.setProgressBar("Saving "
- + (type == jalview.util.ImageMaker.PNG ? "PNG image"
- : "EPS file"), progress);
+ alignFrame.setProgressBar(MessageManager.formatMessage(
+ "status.saving_file",
+ new String[]
+ { type.getLabel() }), progress);
}
try
{
- int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns())
- {
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
- }
-
- int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
- + scalePanel.getHeight();
- int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth);
-
- if (av.getWrapAlignment())
- {
- height = getWrappedHeight();
- if (headless)
- {
- // 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);
- }
- else
- {
- width = seqPanel.getWidth() + getVisibleIdWidth(false);
- }
-
- }
- else if (av.getShowAnnotation())
- {
- height += annotationPanel.adjustPanelHeight() + 3;
- }
-
+ AlignmentDimension aDimension = getAlignmentDimension();
try
{
-
jalview.util.ImageMaker im;
final String imageAction, imageTitle;
- if (type == jalview.util.ImageMaker.PNG)
+ if (type == jalview.util.ImageMaker.TYPE.PNG)
{
imageAction = "Create PNG image from alignment";
imageTitle = null;
}
- else
+ else if (type == jalview.util.ImageMaker.TYPE.EPS)
{
imageAction = "Create EPS file from alignment";
imageTitle = alignFrame.getTitle();
}
- im = new jalview.util.ImageMaker(this, type, imageAction, width,
- height, file, imageTitle);
+ else
+ {
+ imageAction = "Create SVG file from alignment";
+ imageTitle = alignFrame.getTitle();
+ }
+
+ im = new jalview.util.ImageMaker(this, type, imageAction,
+ aDimension.getWidth(), aDimension.getHeight(), file,
+ imageTitle);
if (av.getWrapAlignment())
{
if (im.getGraphics() != null)
{
- printWrappedAlignment(im.getGraphics(), width, height, 0);
+ printWrappedAlignment(im.getGraphics(), aDimension.getWidth(),
+ aDimension.getHeight(), 0);
im.writeImage();
}
}
{
if (im.getGraphics() != null)
{
- printUnwrapped(im.getGraphics(), width, height, 0);
+ printUnwrapped(im.getGraphics(), aDimension.getWidth(),
+ aDimension.getHeight(), 0);
im.writeImage();
}
}
{
if (alignFrame != null && !headless)
{
- alignFrame.setProgressBar("Export complete.", progress);
+ alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress);
+ }
+ }
+ }
+
+ public AlignmentDimension getAlignmentDimension()
+ {
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
+ {
+ maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+ }
+
+ int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
+ + getScalePanel().getHeight();
+ int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth);
+
+ if (av.getWrapAlignment())
+ {
+ height = getWrappedHeight();
+ if (headless)
+ {
+ // 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);
+ }
+ else
+ {
+ width = getSeqPanel().getWidth() + getVisibleIdWidth(false);
}
+
}
+ else if (av.isShowAnnotation())
+ {
+ height += getAnnotationPanel().adjustPanelHeight() + 3;
+ }
+ return new AlignmentDimension(width, height);
+
}
/**
*/
public void makeEPS(File epsFile)
{
- makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
+ makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
}
/**
*/
public void makePNG(File pngFile)
{
- makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile);
+ makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile);
}
+ public void makeSVG(File svgFile)
+ {
+ makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile);
+ }
public void makePNGImageMap(File imgMapFile, String imageName)
{
// /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
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;
}
int annotationHeight = 0;
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
- annotationHeight = annotationPanel.adjustPanelHeight();
+ annotationHeight = getAnnotationPanel().adjustPanelHeight();
}
int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
*/
public void closePanel()
{
- PaintRefresher.RemoveComponent(seqPanel.seqCanvas);
- PaintRefresher.RemoveComponent(idPanel.idCanvas);
+ PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas);
+ PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas());
PaintRefresher.RemoveComponent(this);
if (av != null)
{
jalview.structure.StructureSelectionManager ssm = av
.getStructureSelectionManager();
- ssm.removeStructureViewerListener(seqPanel, null);
- ssm.removeSelectionListener(seqPanel);
+ ssm.removeStructureViewerListener(getSeqPanel(), null);
+ ssm.removeSelectionListener(getSeqPanel());
av.setAlignment(null);
av = null;
}
return av.getAlignment();
}
- /**
- * get the name for this view
- *
- * @return
- */
+
+ @Override
public String getViewName()
{
return av.viewName;
}
public void updateFeatureRenderer(jalview.renderer.seqfeatures.FeatureRenderer fr)
{
- fr.transferSettings(seqPanel.seqCanvas.getFeatureRenderer());
+ fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer());
}
public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr)
{
- if (seqPanel.seqCanvas.getFeatureRenderer() != null)
+ if (getSeqPanel().seqCanvas.getFeatureRenderer() != null)
{
- seqPanel.seqCanvas.getFeatureRenderer().transferSettings(fr);
+ getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr);
}
}
+
+ public ScalePanel getScalePanel()
+ {
+ return scalePanel;
+ }
+
+ public void setScalePanel(ScalePanel scalePanel)
+ {
+ this.scalePanel = scalePanel;
+ }
+
+ public SeqPanel getSeqPanel()
+ {
+ 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;
+ }
}
git://source.jalview.org / jalview.git / blobdiff