/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * 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
+ *
+ * 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.
+ *
+ * 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/>.
*/
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.api.AlignmentViewPanel;
+import jalview.bin.Cache;
import jalview.datamodel.*;
import jalview.jbgui.*;
import jalview.schemes.*;
+import jalview.structure.SelectionSource;
+import jalview.structure.StructureSelectionManager;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.161 $
*/
-public class AlignmentPanel
- extends GAlignmentPanel implements AdjustmentListener, Printable
+public class AlignmentPanel extends GAlignmentPanel implements
+ AdjustmentListener, Printable, AlignmentViewPanel
{
public AlignViewport av;
+
OverviewPanel overviewPanel;
+
SeqPanel seqPanel;
+
IdPanel idPanel;
+
IdwidthAdjuster idwidthAdjuster;
/** DOCUMENT ME!! */
public AlignFrame alignFrame;
+
ScalePanel scalePanel;
+
AnnotationPanel annotationPanel;
+
AnnotationLabels alabels;
// this value is set false when selection area being dragged
boolean fastPaint = true;
+
int hextent = 0;
+
int vextent = 0;
/**
* Creates a new AlignmentPanel object.
- *
- * @param af DOCUMENT ME!
- * @param av DOCUMENT ME!
+ *
+ * @param af
+ * DOCUMENT ME!
+ * @param av
+ * DOCUMENT ME!
*/
public AlignmentPanel(AlignFrame af, final AlignViewport av)
{
{
if (evt.getPropertyName().equals("alignment"))
{
- PaintRefresher.Refresh(ap,
- av.getSequenceSetId(),
- true,
- true);
+ PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true);
alignmentChanged();
}
}
});
-
fontChanged();
adjustAnnotationHeight();
// 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()));
+ 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;
}
/**
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
+ * Calculate the width of the alignment labels based on the displayed names
+ * and any bounds on label width set in preferences.
+ *
+ * @return Dimension giving the maximum width of the alignment label panel
+ * that should be used.
*/
public Dimension calculateIdWidth()
{
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 afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+ int maxwidth = Math.max(20,
+ Math.min(afwidth - 200, (int) 2 * afwidth / 3));
int i = 0;
int idWidth = 0;
String id;
- while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null))
+ while ((i < al.getHeight()) && (al.getSequenceAt(i) != null))
{
SequenceI s = al.getSequenceAt(i);
}
}
- return new Dimension(idWidth, 12);
+ return new Dimension(Math.min(maxwidth, idWidth), 12);
}
/**
- * DOCUMENT ME!
- *
- * @param results DOCUMENT ME!
+ * Highlight the given results on the alignment.
+ *
*/
public void highlightSearchResults(SearchResults results)
{
+ scrollToPosition(results);
seqPanel.seqCanvas.highlightSearchResults(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);
+ }
+ /**
+ * scroll the view to show the position of the highlighted region in results
+ * (if any)
+ *
+ * @param results
+ * @param redrawOverview
+ * - when set, the overview will be recalculated (takes longer)
+ * @return false if results were not found
+ */
+ public boolean scrollToPosition(SearchResults results,
+ boolean redrawOverview)
+ {
+ 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?
- if (results != null)
+ // TODO: tons of nullpointereexceptions raised here.
+ if (results != null && results.getSize() > 0 && av != null
+ && av.alignment != null)
{
- SequenceI seq = results.getResultSequence(0);
- int seqIndex = av.alignment.findIndex(seq);
- int start = seq.findIndex(results.getResultStart(0)) - 1;
- int end = seq.findIndex(results.getResultEnd(0)) - 1;
-
+ int seqIndex = av.alignment.findIndex(results);
+ if (seqIndex == -1)
+ {
+ return false;
+ }
+ SequenceI seq = av.alignment.getSequenceAt(seqIndex);
+
+ int[] r=results.getResults(seq, 0, av.alignment.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;
+ }
+ if (end == seq.getEnd())
+ {
+ return false;
+ }
+ if (av.hasHiddenColumns)
+ {
+ start = av.getColumnSelection().findColumnPosition(start);
+ end = av.getColumnSelection().findColumnPosition(end);
+ if (start==end)
+ {
+ if (!av.colSel.isVisible(r[0]))
+ {
+ // don't scroll - position isn't visible
+ return false;
+ }
+ }
+ }
if (!av.wrapAlignment)
{
- if ( (av.getStartRes() > end) || (av.getEndRes() < start) ||
- ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)))
+ if ((startv = av.getStartRes()) >= start)
+ {
+ setScrollValues(start - 1, seqIndex);
+ }
+ else if ((endv = av.getEndRes()) <= end)
{
- setScrollValues(start, seqIndex);
+ 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);
}
}
else
scrollToWrappedVisible(start);
}
}
-
- paintAlignment(true);
+ if (redrawOverview && overviewPanel != null)
+ {
+ overviewPanel.setBoxPosition();
+ }
+ paintAlignment(redrawOverview);
+ return true;
}
void scrollToWrappedVisible(int res)
{
- int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
- getWidth());
- if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth))
+ int cwidth = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
+ if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth))
{
- vscroll.setValue(res / cwidth);
+ vscroll.setValue((res / cwidth));
av.startRes = vscroll.getValue() * cwidth;
}
+
}
/**
* DOCUMENT ME!
- *
+ *
* @return DOCUMENT ME!
*/
public OverviewPanel getOverviewPanel()
/**
* DOCUMENT ME!
- *
- * @param op DOCUMENT ME!
+ *
+ * @param op
+ * DOCUMENT ME!
*/
public void setOverviewPanel(OverviewPanel op)
{
}
/**
- * DOCUMENT ME!
- *
- * @param b DOCUMENT ME!
+ *
+ * @param b Hide or show annotation panel
+ *
*/
public void setAnnotationVisible(boolean b)
{
repaint();
}
+ /**
+ * automatically adjust annotation panel height for new annotation
+ * whilst ensuring the alignment is still visible.
+ */
public void adjustAnnotationHeight()
{
- //TODO: display vertical annotation scrollbar if necessary
+ // TODO: display vertical annotation scrollbar if necessary
// this is called after loading new annotation onto alignment
if (alignFrame.getHeight() == 0)
{
System.out.println("NEEDS FIXING");
}
-
+ validateAnnotationDimensions(true);
+ addNotify();
+ paintAlignment(true);
+ }
+ /**
+ * calculate the annotation dimensions and refresh slider values accordingly.
+ * need to do repaints/notifys afterwards.
+ */
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
int height = annotationPanel.adjustPanelHeight();
-
+
if (hscroll.isVisible())
{
height += hscroll.getPreferredSize().height;
{
height = alignFrame.getHeight() / 2;
}
-
+ if (!adjustPanelHeight)
+ {
+ // maintain same window layout whilst updating sliders
+ height=annotationScroller.getSize().height;
+ }
hscroll.addNotify();
-
- annotationScroller.setPreferredSize(
- new Dimension(annotationScroller.getWidth(), height));
-
+
+ annotationScroller.setPreferredSize(new Dimension(annotationScroller
+ .getWidth(), height));
annotationSpaceFillerHolder.setPreferredSize(new Dimension(
- annotationSpaceFillerHolder.getWidth(),
- height));
+ annotationSpaceFillerHolder.getWidth(), height));
annotationScroller.validate();// repaint();
- repaint();
+ annotationScroller.addNotify();
}
/**
* DOCUMENT ME!
- *
- * @param wrap DOCUMENT ME!
+ *
+ * @param wrap
+ * DOCUMENT ME!
*/
public void setWrapAlignment(boolean wrap)
{
}
else
{
- if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
+ if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight())
{
return false;
}
/**
* DOCUMENT ME!
- *
- * @param right DOCUMENT ME!
- *
+ *
+ * @param right
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
*/
public boolean scrollRight(boolean right)
}
else
{
- if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
+ if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth())
{
return false;
}
}
/**
- * DOCUMENT ME!
- *
- * @param x DOCUMENT ME!
- * @param y DOCUMENT ME!
+ * Adjust row/column scrollers to show a visible position in the alignment.
+ *
+ * @param x visible column to scroll to
+ * DOCUMENT ME!
+ * @param y visible row to scroll to
+ *
*/
public void setScrollValues(int x, int y)
{
-
+ // System.err.println("Scroll to "+x+","+y);
+ if (av == null || av.alignment == null)
+ {
+ return;
+ }
int width = av.alignment.getWidth();
int height = av.alignment.getHeight();
width = av.getColumnSelection().findColumnPosition(width);
}
- av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
+ av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1);
hextent = seqPanel.seqCanvas.getWidth() / av.charWidth;
vextent = seqPanel.seqCanvas.getHeight() / av.charHeight;
vextent = height;
}
- if ( (hextent + x) > width)
+ if ((hextent + x) > width)
{
x = width - hextent;
}
- if ( (vextent + y) > height)
+ if ((vextent + y) > height)
{
y = height - vextent;
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void adjustmentValueChanged(AdjustmentEvent evt)
{
{
int x = hscroll.getValue();
av.setStartRes(x);
- av.setEndRes( (x +
- (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
+ av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1);
}
if (evt.getSource() == vscroll)
{
if (offy > -1)
{
- int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
- seqCanvas.getWidth());
+ int rowSize = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
av.setStartRes(offy * rowSize);
- av.setEndRes( (offy + 1) * 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
+ // 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()
else
{
av.setStartSeq(offy);
- av.setEndSeq(offy +
- (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
+ av.setEndSeq(offy
+ + (seqPanel.seqCanvas.getHeight() / av.getCharHeight()));
}
}
if (scrollX != 0 || scrollY != 0)
{
idPanel.idCanvas.fastPaint(scrollY);
- seqPanel.seqCanvas.fastPaint(scrollX,
- scrollY);
+ seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
scalePanel.repaint();
if (av.getShowAnnotation())
{
repaint();
- if(updateOverview)
+ if (updateOverview)
{
- jalview.structure.StructureSelectionManager.getStructureSelectionManager()
- .sequenceColoursChanged(this);
+ av.getStructureSelectionManager().sequenceColoursChanged(this);
if (overviewPanel != null)
{
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
*/
public void paintComponent(Graphics g)
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
- int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.
- seqCanvas.getWidth());
+ int canvasWidth = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth());
if (canvasWidth > 0)
{
- int max = maxwidth /
- seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas.
- getWidth()) +
- 1;
+ int max = maxwidth
+ / seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanel.seqCanvas
+ .getWidth()) + 1;
vscroll.setMaximum(max);
vscroll.setUnitIncrement(1);
vscroll.setVisibleAmount(1);
/**
* DOCUMENT ME!
- *
- * @param pg DOCUMENT ME!
- * @param pf DOCUMENT ME!
- * @param pi DOCUMENT ME!
- *
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pf
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
- *
- * @throws PrinterException DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
*/
public int print(Graphics pg, PageFormat pf, int pi)
- throws PrinterException
+ throws PrinterException
{
- pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY());
+ pg.translate((int) pf.getImageableX(), (int) pf.getImageableY());
int pwidth = (int) pf.getImageableWidth();
int pheight = (int) pf.getImageableHeight();
/**
* DOCUMENT ME!
- *
- * @param pg DOCUMENT ME!
- * @param pwidth DOCUMENT ME!
- * @param pheight DOCUMENT ME!
- * @param pi DOCUMENT ME!
- *
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pwidth
+ * DOCUMENT ME!
+ * @param pheight
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
- *
- * @throws PrinterException DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
*/
public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
- throws PrinterException
+ throws PrinterException
{
int idWidth = getVisibleIdWidth();
FontMetrics fm = getFontMetrics(av.getFont());
pg.fillRect(0, 0, pwidth, pheight);
pg.setFont(av.getFont());
- ////////////////////////////////////
- /// How many sequences and residues can we fit on a printable page?
+ // //////////////////////////////////
+ // / 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 = (int) ((pheight - scaleHeight) / av.getCharHeight()) - 1;
int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1;
- /////////////////////////////
- /// Only print these sequences and residues on this page
+ // ///////////////////////////
+ // / Only print these sequences and residues on this page
int startRes;
- /////////////////////////////
- /// Only print these sequences and residues on this page
+ // ///////////////////////////
+ // / Only print these sequences and residues on this page
int endRes;
- /////////////////////////////
- /// Only print these sequences and residues on this page
+ // ///////////////////////////
+ // / Only print these sequences and residues on this page
int startSeq;
- /////////////////////////////
- /// Only print these sequences and residues on this page
+ // ///////////////////////////
+ // / Only print these sequences and residues on this page
int endSeq;
startRes = (pi % pagesWide) * totalRes;
endRes = (startRes + totalRes) - 1;
endSeq = av.getAlignment().getHeight();
}
- int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight;
+ int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
if (av.showAnnotation)
{
return Printable.NO_SUCH_PAGE;
}
- //draw Scale
+ // draw Scale
pg.translate(idWidth, 0);
- scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight);
- pg.translate( -idWidth, scaleHeight);
+ scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth,
+ scaleHeight);
+ pg.translate(-idWidth, scaleHeight);
- ////////////////
+ // //////////////
// Draw the ids
Color currentColor = null;
Color currentTextColor = null;
for (int i = startSeq; i < endSeq; i++)
{
seq = av.getAlignment().getSequenceAt(i);
- if ( (av.getSelectionGroup() != null) &&
- av.getSelectionGroup().getSequences(null).contains(seq))
+ if ((av.getSelectionGroup() != null)
+ && av.getSelectionGroup().getSequences(null).contains(seq))
{
currentColor = Color.gray;
currentTextColor = Color.black;
pg.setColor(currentColor);
pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth,
- av.getCharHeight());
+ av.getCharHeight());
pg.setColor(currentTextColor);
if (av.rightAlignIds)
{
fm = pg.getFontMetrics();
- xPos = idWidth - fm.stringWidth(
- seq.getDisplayId(av.getShowJVSuffix())
- ) - 4;
+ 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.drawString(
+ seq.getDisplayId(av.getShowJVSuffix()),
+ xPos,
+ (((i - startSeq) * av.charHeight) + av.getCharHeight())
+ - (av.getCharHeight() / 5));
}
pg.setFont(av.getFont());
if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
{
- pg.translate( -idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
- alabels.drawComponent( (Graphics2D) pg, idWidth);
+ pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3);
+ alabels.drawComponent((Graphics2D) pg, idWidth);
pg.translate(idWidth + 3, 0);
- annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes +
- 1);
+ annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes + 1);
}
return Printable.PAGE_EXISTS;
/**
* DOCUMENT ME!
- *
- * @param pg DOCUMENT ME!
- * @param pwidth DOCUMENT ME!
- * @param pheight DOCUMENT ME!
- * @param pi DOCUMENT ME!
- *
+ *
+ * @param pg
+ * DOCUMENT ME!
+ * @param pwidth
+ * DOCUMENT ME!
+ * @param pheight
+ * DOCUMENT ME!
+ * @param pi
+ * DOCUMENT ME!
+ *
* @return DOCUMENT ME!
- *
- * @throws PrinterException DOCUMENT ME!
+ *
+ * @throws PrinterException
+ * DOCUMENT ME!
*/
public int printWrappedAlignment(Graphics pg, int pwidth, int pheight,
- int pi)
- throws PrinterException
+ int pi) throws PrinterException
{
int annotationHeight = 0;
hgap += av.charHeight;
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight
- + hgap
- + annotationHeight;
+ int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ + annotationHeight;
int idWidth = getVisibleIdWidth();
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
- int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth -
- idWidth);
+ int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth
+ - idWidth);
int totalHeight = cHeight * (maxwidth / resWidth + 1);
pg.fillRect(0, 0, pwidth, pheight);
pg.setFont(av.getFont());
- ////////////////
+ // //////////////
// Draw the ids
pg.setColor(Color.black);
xPos = idWidth - fm.stringWidth(string) - 4;
}
pg.drawString(string, xPos,
- ( (i * av.charHeight) + ypos + av.charHeight) -
- (av.charHeight / 5));
+ ((i * av.charHeight) + ypos + av.charHeight)
+ - (av.charHeight / 5));
}
if (labels != null)
{
- pg.translate( -3,
- ypos +
- (av.getAlignment().getHeight() * av.charHeight));
+ 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));
+ pg.translate(+3, -ypos
+ - (av.getAlignment().getHeight() * av.charHeight));
}
ypos += cHeight;
- }
- while (ypos < totalHeight);
+ } while (ypos < totalHeight);
pg.translate(idWidth, 0);
- seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0);
+ seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight,
+ 0);
- if ( (pi * pheight) < totalHeight)
+ if ((pi * pheight) < totalHeight)
{
return Printable.PAGE_EXISTS;
int getVisibleIdWidth()
{
- return
- idPanel.getWidth() > 0 ? idPanel.getWidth() :
- calculateIdWidth().width + 4;
+ return idPanel.getWidth() > 0 ? idPanel.getWidth()
+ : calculateIdWidth().width + 4;
}
void makeAlignmentImage(int type, File file)
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
}
- int height = ( (av.alignment.getHeight() + 1) * av.charHeight)
- + scalePanel.getHeight();
+ int height = ((av.alignment.getHeight() + 1) * av.charHeight)
+ + scalePanel.getHeight();
int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
if (av.getWrapAlignment())
{
height = getWrappedHeight();
if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
+ && System.getProperty("java.awt.headless").equals("true"))
{
- width = alignFrame.getWidth()
- - vscroll.getPreferredSize().width
- - alignFrame.getInsets().left
- - alignFrame.getInsets().right;
+ // TODO: JAL-244
+ width = alignFrame.getWidth() - vscroll.getPreferredSize().width
+ - alignFrame.getInsets().left
+ - alignFrame.getInsets().right;
}
else
{
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);
+ 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());
+ im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS,
+ "Create EPS file from alignment", width, height, file,
+ alignFrame.getTitle());
}
if (av.getWrapAlignment())
im.writeImage();
}
}
- }
- catch (OutOfMemoryError err)
+ } catch (OutOfMemoryError err)
{
- System.out.println("########################\n"
- + "OUT OF MEMORY " + file + "\n"
- + "########################");
-
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Out of Memory Creating Image!!"
- +
- "\nSee help files for increasing Java Virtual Machine memory."
- , "Out of memory",
- JOptionPane.WARNING_MESSAGE);
- System.out.println("Create IMAGE: " + err);
- System.gc();
-
- }
- catch (Exception ex)
+ // 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();
}
public void makePNGImageMap(File imgMapFile, String imageName)
{
- ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
- //////////////////////////////////////////////
+ // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
+ // ////////////////////////////////////////////
int idWidth = getVisibleIdWidth();
FontMetrics fm = getFontMetrics(av.getFont());
int scaleHeight = av.charHeight + fm.getDescent();
// Gen image map
- //////////////////////////////////
+ // ////////////////////////////////
if (imgMapFile != null)
{
try
{
- int s, sSize = av.alignment.getHeight(),
- res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy;
+ int s, sSize = av.alignment.getHeight(), res, alwidth = av.alignment
+ .getWidth(), g, gSize, f, fSize, sy;
StringBuffer text = new StringBuffer();
PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
out.println(jalview.io.HTMLOutput.getImageMapHTML());
- out.println("<img src=\"" + imageName +
- "\" border=\"0\" usemap=\"#Map\" >"
- + "<map name=\"Map\">");
+ out.println("<img src=\"" + imageName
+ + "\" border=\"0\" usemap=\"#Map\" >"
+ + "<map name=\"Map\">");
for (s = 0; s < sSize; s++)
{
sy = s * av.charHeight + scaleHeight;
SequenceI seq = av.alignment.getSequenceAt(s);
- SequenceFeature[] features = seq.getDatasetSequence().
- getSequenceFeatures();
+ SequenceFeature[] features = seq.getDatasetSequence()
+ .getSequenceFeatures();
SequenceGroup[] groups = av.alignment.findAllGroups(seq);
for (res = 0; res < alwidth; res++)
{
Object obj = null;
if (av.alignment.isNucleotide())
{
- obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) +
- "");
+ obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
+ + "");
}
else
{
- obj = ResidueProperties.aa2Triplet.get(
- seq.getCharAt(res) + "");
+ obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res)
+ + "");
}
if (obj == null)
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);
+ + (idWidth + res * av.charWidth) + "," + sy + ","
+ + (idWidth + (res + 1) * av.charWidth) + ","
+ + (av.charHeight + sy) + "\""
+ + " onMouseOver=\"toolTip('" + alIndex + " "
+ + triplet);
}
- if (groups[g].getStartRes() < res && groups[g].getEndRes() > res)
+ if (groups[g].getStartRes() < res
+ && groups[g].getEndRes() > res)
{
text.append("<br><em>" + groups[g].getName() + "</em>");
}
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);
+ + (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++)
{
- if ( (features[f].getBegin() <= seq.findPosition(res)) &&
- (features[f].getEnd() >= seq.findPosition(res)))
+ if ((features[f].getBegin() <= seq.findPosition(res))
+ && (features[f].getEnd() >= seq.findPosition(res)))
{
if (features[f].getType().equals("disulfide bond"))
{
if (features[f].getBegin() == seq.findPosition(res)
- || features[f].getEnd() == seq.findPosition(res))
+ || features[f].getEnd() == seq
+ .findPosition(res))
{
- text.append("<br>disulfide bond " + features[f].getBegin() +
- ":" +
- features[f].getEnd());
+ text.append("<br>disulfide bond "
+ + features[f].getBegin() + ":"
+ + features[f].getEnd());
}
}
else
{
text.append("<br>");
text.append(features[f].getType());
- if (features[f].getDescription() != null &&
- !features[f].
- getType().equals(features[f].getDescription()))
+ 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") + ")");
+ text.append(" (" + features[f].getValue("status")
+ + ")");
}
}
}
out.println("</map></body></html>");
out.close();
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
ex.printStackTrace();
}
- } ///////////END OF IMAGE MAP
+ } // /////////END OF IMAGE MAP
}
int seqPanelWidth = seqPanel.seqCanvas.getWidth();
if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
+ && System.getProperty("java.awt.headless").equals("true"))
{
- seqPanelWidth = alignFrame.getWidth()
- - getVisibleIdWidth()
- - vscroll.getPreferredSize().width
- - alignFrame.getInsets().left
- - alignFrame.getInsets().right;
+ seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
+ - vscroll.getPreferredSize().width
+ - alignFrame.getInsets().left - alignFrame.getInsets().right;
}
- int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(
- seqPanelWidth
- );
+ int chunkWidth = seqPanel.seqCanvas
+ .getWrappedCanvasWidth(seqPanelWidth);
int hgap = av.charHeight;
if (av.scaleAboveWrapped)
annotationHeight = annotationPanel.adjustPanelHeight();
}
- int cHeight = av.getAlignment().getHeight() * av.charHeight
- + hgap
- + annotationHeight;
+ int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ + annotationHeight;
int maxwidth = av.alignment.getWidth();
if (av.hasHiddenColumns)
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
- int height = ( (maxwidth / chunkWidth) + 1) * cHeight;
+ int height = ((maxwidth / chunkWidth) + 1) * cHeight;
return height;
}
+
+ /**
+ * close the panel - deregisters all listeners and nulls any references to
+ * alignment data.
+ */
+ public void closePanel()
+ {
+ PaintRefresher.RemoveComponent(seqPanel.seqCanvas);
+ PaintRefresher.RemoveComponent(idPanel.idCanvas);
+ PaintRefresher.RemoveComponent(this);
+ if (av != null)
+ {
+ jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager();
+ ssm.removeStructureViewerListener(seqPanel, null);
+ ssm.removeSelectionListener(seqPanel);
+ av.alignment = null;
+ av = null;
+ }
+ else
+ {
+ if (Cache.log.isDebugEnabled())
+ {
+ Cache.log.warn("Closing alignment panel which is already closed.");
+ }
+ }
+ }
+
+ /**
+ * hides or shows dynamic annotation rows based on groups and av state flags
+ */
+ public void updateAnnotation()
+ {
+ updateAnnotation(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 sortg = true;
+
+ // remove old automatic annotation
+ // add any new annotation
+
+ Vector gr = av.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray());
+ // intersect alignment annotation with alignment groups
+
+ AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation();
+ Hashtable oldrfs = new Hashtable();
+ if (aan != null)
+ {
+ for (int an = 0; an < aan.length; an++)
+ {
+ if (aan[an].autoCalculated && aan[an].groupRef != null)
+ {
+ oldrfs.put(aan[an].groupRef, aan[an].groupRef);
+ av.alignment.deleteAnnotation(aan[an]);
+ aan[an] = null;
+ }
+ }
+ }
+ SequenceGroup sg;
+ if (gr != null)
+ {
+ for (int g = 0; g < gr.size(); g++)
+ {
+ updateCalcs = false;
+ sg = (SequenceGroup) gr.elementAt(g);
+ if (applyGlobalSettings || !oldrfs.containsKey(sg))
+ {
+ // set defaults for this group's conservation/consensus
+ sg.setshowSequenceLogo(showprf);
+ sg.setShowConsensusHistogram(showConsHist);
+ }
+ if (conv)
+ {
+ updateCalcs = true;
+ av.alignment.addAnnotation(sg.getConservationRow(), 0);
+ }
+ if (cons)
+ {
+ updateCalcs = true;
+ av.alignment.addAnnotation(sg.getConsensus(), 0);
+ }
+ // refresh the annotation rows
+ if (updateCalcs)
+ {
+ sg.recalcConservation();
+ }
+ }
+ }
+ oldrfs.clear();
+ adjustAnnotationHeight();
+ }
+
+ @Override
+ public AlignmentI getAlignment()
+ {
+ return av.alignment;
+ }
+
+ /**
+ * get the name for this view
+ * @return
+ */
+ public String getViewName()
+ {
+ return av.viewName;
+ }
+
+ /**
+ * Make/Unmake this alignment panel the current input focus
+ * @param b
+ */
+ public void setSelected(boolean b)
+ {
+ try {
+ alignFrame.setSelected(b);
+ } catch (Exception ex) {};
+
+ if (b)
+ {
+ alignFrame.setDisplayedView(this);
+ }
+ }
+
+ @Override
+ public StructureSelectionManager getStructureSelectionManager()
+ {
+ return av.getStructureSelectionManager();
+ }
}
git://source.jalview.org / jalview.git / blobdiff