/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
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
+ AdjustmentListener, Printable, AlignmentViewPanel
{
public AlignViewport av;
*/
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);
+ }
+ /**
+ * 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
+ * @return Dimension giving the maximum width of the alignment label panel
+ * that should be used.
+ */
+ public Dimension calculateIdWidth(int maxwidth)
+ {
Container c = new Container();
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;
}
}
- return new Dimension(Math.min(maxwidth, idWidth), 12);
+ return new Dimension(maxwidth<0 ? idWidth : Math.min(maxwidth, idWidth), 12);
}
/**
// do we need to scroll the panel?
// TODO: tons of nullpointereexceptions raised here.
if (results != null && results.getSize() > 0 && av != null
- && av.alignment != null)
+ && av.getAlignment() != null)
{
- int seqIndex = av.alignment.findIndex(results);
+ int seqIndex = av.getAlignment().findIndex(results);
if (seqIndex == -1)
{
return false;
}
- SequenceI seq = av.alignment.getSequenceAt(seqIndex);
+ SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
- int[] r=results.getResults(seq, 0, av.alignment.getWidth());
+ int[] r=results.getResults(seq, 0, av.getAlignment().getWidth());
if (r == null)
{
return false;
{
return false;
}
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
start = av.getColumnSelection().findColumnPosition(start);
end = av.getColumnSelection().findColumnPosition(end);
if (start==end)
{
- if (!av.colSel.isVisible(r[0]))
+ if (!av.getColumnSelection().isVisible(r[0]))
{
// don't scroll - position isn't visible
return false;
scrollToWrappedVisible(start);
}
}
- if (!redrawOverview && overviewPanel != null)
+ if (redrawOverview && overviewPanel != null)
{
overviewPanel.setBoxPosition();
}
- paintAlignment(!redrawOverview);
+ paintAlignment(redrawOverview);
return true;
}
}
/**
- * 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
{
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));
annotationSpaceFillerHolder.setPreferredSize(new Dimension(
annotationSpaceFillerHolder.getWidth(), height));
annotationScroller.validate();// repaint();
- addNotify();
- repaint();
+ annotationScroller.addNotify();
}
/**
public void setScrollValues(int x, int y)
{
// System.err.println("Scroll to "+x+","+y);
- if (av == null || av.alignment == null)
+ if (av == null || av.getAlignment() == null)
{
return;
}
- int width = av.alignment.getWidth();
- int height = av.alignment.getHeight();
+ int width = av.getAlignment().getWidth();
+ int height = av.getAlignment().getHeight();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
width = av.getColumnSelection().findColumnPosition(width);
}
if (updateOverview)
{
- jalview.structure.StructureSelectionManager
- .getStructureSelectionManager().sequenceColoursChanged(this);
+ av.getStructureSelectionManager().sequenceColoursChanged(this);
if (overviewPanel != null)
{
if (av.getWrapAlignment())
{
- int maxwidth = av.alignment.getWidth();
+ int maxwidth = av.getAlignment().getWidth();
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi)
throws PrinterException
{
- int idWidth = getVisibleIdWidth();
+ int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
int scaleHeight = av.charHeight + fm.getDescent();
endSeq = av.getAlignment().getHeight();
}
- int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight;
+ int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1) * pheight;
if (av.showAnnotation)
{
pg.translate(idWidth, 0);
seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0);
- if (av.showAnnotation && (endSeq == av.alignment.getHeight()))
+ 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.drawComponent((Graphics2D) pg, startRes, endRes + 1);
+ annotationPanel.renderer.drawComponent(annotationPanel, av, (Graphics2D) pg, -1, startRes, endRes + 1);
}
return Printable.PAGE_EXISTS;
int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ annotationHeight;
- int idWidth = getVisibleIdWidth();
+ int idWidth = getVisibleIdWidth(false);
- int maxwidth = av.alignment.getWidth();
- if (av.hasHiddenColumns)
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
do
{
- for (int i = 0; i < av.alignment.getHeight(); i++)
+ for (int i = 0; i < av.getAlignment().getHeight(); i++)
{
pg.setFont(idPanel.idCanvas.idfont);
- SequenceI s = av.alignment.getSequenceAt(i);
+ SequenceI s = av.getAlignment().getSequenceAt(i);
String string = s.getDisplayId(av.getShowJVSuffix());
int xPos = 0;
if (av.rightAlignIds)
return Printable.NO_SUCH_PAGE;
}
}
-
+ /**
+ * get current sequence ID panel width, or nominal value if panel were to be displayed using default settings
+ * @return
+ */
int getVisibleIdWidth()
{
- return idPanel.getWidth() > 0 ? idPanel.getWidth()
- : calculateIdWidth().width + 4;
+ 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
+ * @return
+ */
+ 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;
+ }
+ Integer idwidth=null;
+ if (onscreen || (idwidth=Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"))==null) {
+ return (idPanel.getWidth() > 0 ? idPanel.getWidth()
+ : calculateIdWidth().width + 4);
+ }
+ return idwidth.intValue()+4;
}
void makeAlignmentImage(int type, File file)
{
- int maxwidth = av.alignment.getWidth();
- if (av.hasHiddenColumns)
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
}
- int height = ((av.alignment.getHeight() + 1) * av.charHeight)
+ int height = ((av.getAlignment().getHeight() + 1) * av.charHeight)
+ scalePanel.getHeight();
- int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
+ int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth);
if (av.getWrapAlignment())
{
if (System.getProperty("java.awt.headless") != null
&& System.getProperty("java.awt.headless").equals("true"))
{
+ // 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;
+ - alignFrame.getInsets().right
+ - getVisibleIdWidth()+getVisibleIdWidth(false);
}
else
{
- width = seqPanel.getWidth() + getVisibleIdWidth();
+ width = seqPanel.getWidth() + getVisibleIdWidth(false);
}
}
{
// /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS
// ////////////////////////////////////////////
- int idWidth = getVisibleIdWidth();
+ int idWidth = getVisibleIdWidth(false);
FontMetrics fm = getFontMetrics(av.getFont());
int scaleHeight = av.charHeight + fm.getDescent();
{
try
{
- int s, sSize = av.alignment.getHeight(), res, alwidth = av.alignment
+ int s, sSize = av.getAlignment().getHeight(), res, alwidth = av.getAlignment()
.getWidth(), g, gSize, f, fSize, sy;
StringBuffer text = new StringBuffer();
PrintWriter out = new PrintWriter(new FileWriter(imgMapFile));
{
sy = s * av.charHeight + scaleHeight;
- SequenceI seq = av.alignment.getSequenceAt(s);
+ SequenceI seq = av.getAlignment().getSequenceAt(s);
SequenceFeature[] features = seq.getDatasetSequence()
.getSequenceFeatures();
- SequenceGroup[] groups = av.alignment.findAllGroups(seq);
+ SequenceGroup[] groups = av.getAlignment().findAllGroups(seq);
for (res = 0; res < alwidth; res++)
{
text = new StringBuffer();
Object obj = null;
- if (av.alignment.isNucleotide())
+ if (av.getAlignment().isNucleotide())
{
obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res)
+ "");
int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap
+ annotationHeight;
- int maxwidth = av.alignment.getWidth();
- if (av.hasHiddenColumns)
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
{
maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1;
}
*/
public void closePanel()
{
- jalview.structure.StructureSelectionManager ssm = jalview.structure.StructureSelectionManager
- .getStructureSelectionManager();
- ssm.removeStructureViewerListener(seqPanel, null);
- ssm.removeSelectionListener(seqPanel);
PaintRefresher.RemoveComponent(seqPanel.seqCanvas);
PaintRefresher.RemoveComponent(idPanel.idCanvas);
PaintRefresher.RemoveComponent(this);
if (av != null)
{
- av.alignment = null;
+ jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager();
+ ssm.removeStructureViewerListener(seqPanel, null);
+ ssm.removeSelectionListener(seqPanel);
+ av.setAlignment(null);
av = null;
}
else
boolean cons = av.isShowGroupConsensus();
boolean showprf = av.isShowSequenceLogo();
boolean showConsHist = av.isShowConsensusHistogram();
+ boolean normLogo = av.isNormaliseSequenceLogo();
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();
+ AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation();
Hashtable oldrfs = new Hashtable();
if (aan != null)
{
if (aan[an].autoCalculated && aan[an].groupRef != null)
{
oldrfs.put(aan[an].groupRef, aan[an].groupRef);
- av.alignment.deleteAnnotation(aan[an]);
+ av.getAlignment().deleteAnnotation(aan[an]);
aan[an] = null;
}
}
}
- SequenceGroup sg;
- if (gr != null)
+ if (av.getAlignment().getGroups()!=null)
{
- for (int g = 0; g < gr.size(); g++)
+ for (SequenceGroup sg:av.getAlignment().getGroups())
{
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);
+ sg.setNormaliseSequenceLogo(normLogo);
}
if (conv)
{
updateCalcs = true;
- av.alignment.addAnnotation(sg.getConservationRow(), 0);
+ av.getAlignment().addAnnotation(sg.getConservationRow(), 0);
}
if (cons)
{
updateCalcs = true;
- av.alignment.addAnnotation(sg.getConsensus(), 0);
+ av.getAlignment().addAnnotation(sg.getConsensus(), 0);
}
// refresh the annotation rows
if (updateCalcs)
oldrfs.clear();
adjustAnnotationHeight();
}
+
+ @Override
+ public AlignmentI getAlignment()
+ {
+ return av.getAlignment();
+ }
+
+ /**
+ * 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();
+ }
+
+ @Override
+ public void raiseOOMWarning(String string, OutOfMemoryError error)
+ {
+ new OOMWarning(string, error, this);
+ }
}
git://source.jalview.org / jalview.git / blobdiff