X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=190682941a129aca2ff76b5377fa7860c4c803a1;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=671a7cba64b47fcb147f44f7ab6be136f7dd4223;hpb=23b954d9c84a16a7dc12ab331a01e44d5e0e5cd4;p=jalview.git
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 671a7cb..1906829 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -1,37 +1,62 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.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.AlignViewportI;
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 jalview.util.Platform;
+
+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.Insets;
+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 java.util.List;
+
+import javax.swing.SwingUtilities;
/**
* DOCUMENT ME!
@@ -46,20 +71,22 @@ public class AlignmentPanel extends GAlignmentPanel implements
OverviewPanel overviewPanel;
- SeqPanel seqPanel;
+ private SeqPanel seqPanel;
+
+ private IdPanel idPanel;
- 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;
@@ -68,40 +95,42 @@ public class AlignmentPanel extends GAlignmentPanel implements
int vextent = 0;
+ /*
+ * Flag set while scrolling to follow complementary cDNA/protein scroll. When
+ * true, suppresses invoking the same method recursively.
+ */
+ private boolean followingComplementScroll;
+
/**
* Creates a new AlignmentPanel object.
*
* @param af
- * DOCUMENT ME!
* @param av
- * DOCUMENT ME!
*/
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
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);
@@ -119,7 +148,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
});
fontChanged();
adjustAnnotationHeight();
+ updateLayout();
+ }
+ @Override
+ public AlignViewportI getAlignViewport()
+ {
+ return av;
}
public void alignmentChanged()
@@ -141,24 +176,29 @@ public class AlignmentPanel extends GAlignmentPanel implements
// 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
+ scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight()
+ fm.getDescent()));
+ idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av
+ .getCharHeight() + 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)
{
overviewPanel.setBoxPosition();
}
+ if (this.alignFrame.getSplitViewContainer() != null)
+ {
+ ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout();
+ }
repaint();
}
@@ -173,11 +213,21 @@ public class AlignmentPanel extends GAlignmentPanel implements
public Dimension calculateIdWidth()
{
// 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 maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3));
+ r = calculateIdWidth(maxwidth);
+ av.setIdWidth(r.width);
+ }
+ else
+ {
+ r = new Dimension();
+ r.width = av.getIdWidth();
+ r.height = 0;
+ }
+ return r;
}
/**
@@ -220,7 +270,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
if (al.getAlignmentAnnotation() != null)
{
- fm = c.getFontMetrics(alabels.getFont());
+ fm = c.getFontMetrics(getAlabels().getFont());
while (i < al.getAlignmentAnnotation().length)
{
@@ -246,37 +296,56 @@ public class AlignmentPanel extends GAlignmentPanel implements
public void highlightSearchResults(SearchResults results)
{
scrollToPosition(results);
- seqPanel.seqCanvas.highlightSearchResults(results);
+ getSeqPanel().seqCanvas.highlightSearchResults(results);
}
/**
- * scroll the view to show the position of the highlighted region in results
+ * Scroll the view to show the position of the highlighted region in results
* (if any) and redraw the overview
*
* @param results
*/
public boolean scrollToPosition(SearchResults results)
{
- return scrollToPosition(results, true);
+ return scrollToPosition(results, 0, true, false);
}
/**
- * scroll the view to show the position of the highlighted region in results
+ * Scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
+ * @param searchResults
+ * @param redrawOverview
+ * @return
+ */
+ public boolean scrollToPosition(SearchResults searchResults,
+ boolean redrawOverview)
+ {
+ return scrollToPosition(searchResults, 0, redrawOverview, false);
+ }
+
+ /**
+ * Scroll the view to show the position of the highlighted region in results
* (if any)
*
* @param results
+ * @param verticalOffset
+ * if greater than zero, allows scrolling to a position below the
+ * first displayed sequence
* @param redrawOverview
* - when set, the overview will be recalculated (takes longer)
+ * @param centre
+ * if true, try to centre the search results horizontally in the view
* @return false if results were not found
*/
public boolean scrollToPosition(SearchResults results,
- boolean redrawOverview)
+ int verticalOffset, boolean redrawOverview, boolean centre)
{
- int startv, endv, starts, ends, width;
+ int startv, endv, starts, ends;
// 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.
+ // TODO: tons of nullpointerexceptions raised here.
if (results != null && results.getSize() > 0 && av != null
&& av.getAlignment() != null)
{
@@ -294,8 +363,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
}
int start = r[0];
int end = r[1];
- // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); //
// DEBUG
+ // System.err.println(this.av.viewName + " Seq : " + seqIndex
+ // + " Scroll to " + start + "," + end);
+
+ /*
+ * 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 = end + offset - 1;
+ }
if (start < 0)
{
return false;
@@ -317,24 +398,50 @@ public class AlignmentPanel extends GAlignmentPanel implements
}
}
}
- if (!av.wrapAlignment)
+
+ /*
+ * allow for offset of target sequence (actually scroll to one above it)
+ */
+ seqIndex = Math.max(0, seqIndex - verticalOffset);
+
+ // System.out.println("start=" + start + ", end=" + end + ", startv="
+ // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts="
+ // + av.getStartSeq() + ", ends=" + av.getEndSeq());
+ if (!av.getWrapAlignment())
{
if ((startv = av.getStartRes()) >= start)
{
- setScrollValues(start - 1, seqIndex);
+ /*
+ * Scroll left to make start of search results visible
+ */
+ // setScrollValues(start - 1, seqIndex); // plus one residue
+ setScrollValues(start, seqIndex);
}
else if ((endv = av.getEndRes()) <= end)
{
- setScrollValues(startv + 1 + end - endv, seqIndex);
+ /*
+ * Scroll right to make end of search results visible
+ */
+ // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one
+ setScrollValues(startv + end - endv, seqIndex);
}
else if ((starts = av.getStartSeq()) > seqIndex)
{
+ /*
+ * 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
{
@@ -351,8 +458,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
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));
@@ -390,7 +497,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
*/
public void setAnnotationVisible(boolean b)
{
- if (!av.wrapAlignment)
+ if (!av.getWrapAlignment())
{
annotationSpaceFillerHolder.setVisible(b);
annotationScroller.setVisible(b);
@@ -421,54 +528,61 @@ public class AlignmentPanel extends GAlignmentPanel implements
*/
protected void validateAnnotationDimensions(boolean adjustPanelHeight)
{
- int height = annotationPanel.adjustPanelHeight();
-
- int theight = av.getCharHeight() * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0 : av.getAlignment().getHiddenSequences().getSize()));
- float sscaling = (float) (theight/(1.0*theight+height));
- float ascaling=(float)(height*1.0/alignFrame.getHeight());
- int rheight = alignFrame.getHeight() - height - av.getCharHeight();
+ int annotationHeight = getAnnotationPanel().adjustPanelHeight();
+
if (adjustPanelHeight)
{
- // NOTE: this logic is different in the applet. Need a better algorithm to define behaviour
- // try and set height according to alignment
- if (ascaling>0 && sscaling < 0.5)
+ int rowHeight = av.getCharHeight();
+ int alignmentHeight = rowHeight * av.getAlignment().getHeight();
+
+ /*
+ * Estimate available height in the AlignFrame for alignment +
+ * annotations. Deduct an estimate for title bar, menu bar, scale panel,
+ * hscroll, status bar (as these are not laid out we can't inspect their
+ * actual heights). Insets gives frame borders.
+ */
+ int stuff = Platform.isAMac() ? 80 : 100;
+ Insets insets = alignFrame.getInsets();
+ int availableHeight = alignFrame.getHeight() - stuff - insets.top
+ - insets.bottom;
+
+ /*
+ * If not enough vertical space, maximize annotation height while keeping
+ * at least two rows of alignment visible
+ */
+ if (annotationHeight + alignmentHeight > availableHeight)
{
- // if the alignment is too big then
- // default is 0.5 split
- height = alignFrame.getHeight() / 2;
- }
- else
- {
- // if space for more than one sequence row left when annotation is fully displayed then set height to annotation height
- // otherwise, leave at least two lines of sequence shown.
- height = (rheight>av.getCharHeight()) ? height : (-av.getCharHeight() * 3
- + (int) (alignFrame.getHeight() * (1 - sscaling)));
+ annotationHeight = Math.min(annotationHeight, availableHeight - 2
+ * rowHeight);
}
}
else
{
// maintain same window layout whilst updating sliders
- height = annotationScroller.getSize().height;
+ annotationHeight = annotationScroller.getSize().height;
}
hscroll.addNotify();
annotationScroller.setPreferredSize(new Dimension(annotationScroller
- .getWidth(), height));
+ .getWidth(), 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()
{
+ fontChanged();
+ setAnnotationVisible(av.isShowAnnotation());
+ boolean wrap = av.getWrapAlignment();
av.startSeq = 0;
scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
@@ -479,7 +593,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
annotationScroller.setVisible(false);
annotationSpaceFillerHolder.setVisible(false);
}
- else if (av.showAnnotation)
+ else if (av.isShowAnnotation())
{
annotationScroller.setVisible(true);
annotationSpaceFillerHolder.setVisible(true);
@@ -559,14 +673,14 @@ public class AlignmentPanel extends GAlignmentPanel implements
* Adjust row/column scrollers to show a visible position in the alignment.
*
* @param x
- * visible column to scroll to DOCUMENT ME!
+ * visible column to scroll to
* @param y
* visible row to scroll to
*
*/
public void setScrollValues(int x, int y)
{
- // System.err.println("Scroll to "+x+","+y);
+ // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y);
if (av == null || av.getAlignment() == null)
{
return;
@@ -579,10 +693,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
width = av.getColumnSelection().findColumnPosition(width);
}
- av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
+ av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av
+ .getCharWidth())) - 1);
- hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
- vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
+ hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth();
+ vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight();
if (hextent > width)
{
@@ -626,7 +741,6 @@ public class AlignmentPanel extends GAlignmentPanel implements
*/
public void adjustmentValueChanged(AdjustmentEvent evt)
{
-
int oldX = av.getStartRes();
int oldY = av.getStartSeq();
@@ -634,7 +748,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
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)
@@ -645,8 +760,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
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);
}
@@ -668,7 +783,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
av.setStartSeq(offy);
av.setEndSeq(offy
- + (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
+ + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight()));
}
}
@@ -699,24 +814,45 @@ public class AlignmentPanel extends GAlignmentPanel implements
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);
}
}
}
+ /*
+ * If there is one, scroll the (Protein/cDNA) complementary alignment to
+ * match, unless we are ourselves doing that.
+ */
+ if (isFollowingComplementScroll())
+ {
+ setFollowingComplementScroll(false);
+ }
+ else
+ {
+ av.scrollComplementaryAlignment();
+ }
}
+ /**
+ * 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)
{
+ // TODO: determine if this paintAlignment changed structure colours
av.getStructureSelectionManager().sequenceColoursChanged(this);
if (overviewPanel != null)
@@ -736,7 +872,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
invalidate();
- Dimension d = idPanel.idCanvas.getPreferredSize();
+ Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
idPanelHolder.setPreferredSize(d);
hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
validate();
@@ -750,13 +886,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
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);
@@ -824,7 +960,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
+ int scaleHeight = av.getCharHeight() + fm.getDescent();
pg.setColor(Color.white);
pg.fillRect(0, 0, pwidth, pheight);
@@ -834,7 +970,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
// / 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;
@@ -872,9 +1008,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1)
* pheight;
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
- pagesHigh += annotationPanel.adjustPanelHeight() + 3;
+ pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3;
}
pagesHigh /= pheight;
@@ -886,7 +1022,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
// 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);
@@ -895,7 +1031,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
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++)
@@ -914,13 +1050,13 @@ public class AlignmentPanel extends GAlignmentPanel implements
}
pg.setColor(currentColor);
- pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
+ pg.fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth,
av.getCharHeight());
pg.setColor(currentTextColor);
int xPos = 0;
- if (av.rightAlignIds)
+ if (av.isRightAlignIds())
{
fm = pg.getFontMetrics();
xPos = idWidth
@@ -928,10 +1064,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
- 4;
}
- pg.drawString(
- seq.getDisplayId(av.getShowJVSuffix()),
- xPos,
- (((i - startSeq) * av.charHeight) + av.getCharHeight())
+ pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos,
+ (((i - startSeq) * av.getCharHeight()) + av.getCharHeight())
- (av.getCharHeight() / 5));
}
@@ -939,18 +1073,20 @@ public class AlignmentPanel extends GAlignmentPanel implements
// 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);
+ pg.translate(-idWidth - 3, (endSeq - startSeq) * av.getCharHeight()
+ + 3);
+ 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);
}
@@ -977,22 +1113,21 @@ public class AlignmentPanel extends GAlignmentPanel implements
public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
int pi) throws PrinterException
{
-
int annotationHeight = 0;
AnnotationLabels labels = null;
- if (av.showAnnotation)
+ if (av.isShowAnnotation())
{
- annotationHeight = annotationPanel.adjustPanelHeight();
+ annotationHeight = getAnnotationPanel().adjustPanelHeight();
labels = new AnnotationLabels(av);
}
- 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);
@@ -1003,7 +1138,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
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);
@@ -1026,28 +1161,31 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
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.drawString(string, xPos,
- ((i * av.charHeight) + ypos + av.charHeight)
- - (av.charHeight / 5));
+ ((i * av.getCharHeight()) + ypos + av.getCharHeight())
+ - (av.getCharHeight() / 5));
}
if (labels != null)
{
- pg.translate(-3, ypos
- + (av.getAlignment().getHeight() * av.charHeight));
+ pg.translate(-3,
+ ypos + (av.getAlignment().getHeight() * av.getCharHeight()));
pg.setFont(av.getFont());
labels.drawComponent(pg, idWidth);
- pg.translate(+3, -ypos
- - (av.getAlignment().getHeight() * av.charHeight));
+ pg.translate(
+ +3,
+ -ypos
+ - (av.getAlignment().getHeight() * av
+ .getCharHeight()));
}
ypos += cHeight;
@@ -1055,8 +1193,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
pg.translate(idWidth, 0);
- seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
- 0);
+ getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth,
+ totalHeight, 0);
if ((pi * pheight) < totalHeight)
{
@@ -1075,7 +1213,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
*
* @return
*/
- int getVisibleIdWidth()
+ public int getVisibleIdWidth()
{
return getVisibleIdWidth(true);
}
@@ -1089,7 +1227,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
* 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))
@@ -1100,82 +1238,55 @@ public class AlignmentPanel extends GAlignmentPanel implements
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.getProperty("java.awt.headless").equals("true"));
+ 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 Object[] { 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();
}
}
@@ -1183,7 +1294,8 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
if (im.getGraphics() != null)
{
- printUnwrapped(im.getGraphics(), width, height, 0);
+ printUnwrapped(im.getGraphics(), aDimension.getWidth(),
+ aDimension.getHeight(), 0);
im.writeImage();
}
}
@@ -1202,9 +1314,51 @@ public class AlignmentPanel extends GAlignmentPanel implements
{
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.getCharHeight())
+ + getScalePanel().getHeight();
+ int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth());
+
+ 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);
+
}
/**
@@ -1212,7 +1366,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
*/
public void makeEPS(File epsFile)
{
- makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile);
+ makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile);
}
/**
@@ -1220,7 +1374,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
*/
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)
@@ -1229,7 +1388,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
// ////////////////////////////////////////////
int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
- int scaleHeight = av.charHeight + fm.getDescent();
+ int scaleHeight = av.getCharHeight() + fm.getDescent();
// Gen image map
// ////////////////////////////////
@@ -1248,33 +1407,31 @@ public class AlignmentPanel extends GAlignmentPanel implements
for (s = 0; s < sSize; s++)
{
- sy = s * av.charHeight + scaleHeight;
+ sy = s * av.getCharHeight() + scaleHeight;
SequenceI seq = av.getAlignment().getSequenceAt(s);
- SequenceFeature[] features = seq.getDatasetSequence()
- .getSequenceFeatures();
+ SequenceFeature[] features = seq.getSequenceFeatures();
SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
for (res = 0; res < alwidth; res++)
{
text = new StringBuffer();
- Object obj = null;
+ String triplet = null;
if (av.getAlignment().isNucleotide())
{
- obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
- + "");
+ triplet = ResidueProperties.nucleotideName.get(seq
+ .getCharAt(res) + "");
}
else
{
- obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+ triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+ "");
}
- 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++)
@@ -1282,9 +1439,9 @@ public class AlignmentPanel extends GAlignmentPanel implements
if (text.length() < 1)
{
text.append(" seqs = av.getAlignment().getSequences();
+
+ /*
+ * This is like AlignmentI.findIndex(seq) but here we are matching the
+ * dataset sequence not the aligned sequence
+ */
+ boolean matched = false;
+ for (SequenceI seq : seqs)
{
- seqPanel.seqCanvas.getFeatureRenderer().transferSettings(fr);
+ if (mappedTo == seq.getDatasetSequence())
+ {
+ matched = true;
+ break;
+ }
}
+ if (!matched)
+ {
+ return; // failsafe, shouldn't happen
+ }
+
+ /*
+ * Scroll to position but centring the target residue.
+ */
+ scrollToPosition(sr, verticalOffset, true, true);
+ }
+
+ /**
+ * Set a flag to say we are scrolling to follow a (cDNA/protein) complement.
+ *
+ * @param b
+ */
+ protected void setFollowingComplementScroll(boolean b)
+ {
+ this.followingComplementScroll = b;
+ }
+
+ protected boolean isFollowingComplementScroll()
+ {
+ return this.followingComplementScroll;
}
}