/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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.
- *
+ *
* 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.beans.*;
import java.io.*;
-import java.util.Hashtable;
-import java.util.Vector;
import java.awt.*;
import java.awt.event.*;
import jalview.datamodel.*;
import jalview.jbgui.*;
import jalview.schemes.*;
-import jalview.structure.SelectionSource;
import jalview.structure.StructureSelectionManager;
/**
*/
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);
-
- int[] r=results.getResults(seq, 0, av.alignment.getWidth());
+ SequenceI seq = av.getAlignment().getSequenceAt(seqIndex);
+
+ 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 (start == end)
{
- if (!av.colSel.isVisible(r[0]))
+ if (!av.getColumnSelection().isVisible(r[0]))
{
// don't scroll - position isn't visible
return false;
/**
*
- * @param b Hide or show annotation panel
- *
+ * @param b
+ * Hide or show annotation panel
+ *
*/
public void setAnnotationVisible(boolean b)
{
}
/**
- * automatically adjust annotation panel height for new annotation
- * whilst ensuring the alignment is still visible.
+ * automatically adjust annotation panel height for new annotation whilst
+ * ensuring the alignment is still visible.
*/
public void adjustAnnotationHeight()
{
addNotify();
paintAlignment(true);
}
+
/**
* calculate the annotation dimensions and refresh slider values accordingly.
- * need to do repaints/notifys afterwards.
+ * need to do repaints/notifys afterwards.
*/
- protected void validateAnnotationDimensions(boolean adjustPanelHeight) {
+ protected void validateAnnotationDimensions(boolean adjustPanelHeight)
+ {
int height = annotationPanel.adjustPanelHeight();
-
+
if (hscroll.isVisible())
{
height += hscroll.getPreferredSize().height;
if (!adjustPanelHeight)
{
// maintain same window layout whilst updating sliders
- height=annotationScroller.getSize().height;
+ height = annotationScroller.getSize().height;
}
hscroll.addNotify();
-
+
annotationScroller.setPreferredSize(new Dimension(annotationScroller
.getWidth(), height));
/**
* 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
- *
+ * @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)
+ 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);
}
seqPanel.seqCanvas.fastPaint(scrollX, scrollY);
scalePanel.repaint();
- if (av.getShowAnnotation())
+ if (av.getShowAnnotation() && scrollX!=0)
{
annotationPanel.fastPaint(scrollX);
}
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()))
{
+ // draw annotation - need to offset for current scroll position
+ int offset = -alabels.scrollOffset;
+ pg.translate(0, offset);
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);
+ pg.translate(0, -offset);
}
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)
}
}
+ /**
+ * 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);
}
- void makeAlignmentImage(int type, File file)
+ /**
+ * 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)
{
- int maxwidth = av.alignment.getWidth();
- if (av.hasHiddenColumns)
+ // see if rendering offscreen - check preferences and calc width accordingly
+ if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
{
- maxwidth = av.getColumnSelection().findColumnPosition(maxwidth);
+ return calculateIdWidth(-1).width + 4;
}
-
- int height = ((av.alignment.getHeight() + 1) * av.charHeight)
- + scalePanel.getHeight();
- int width = getVisibleIdWidth() + (maxwidth * av.charWidth);
-
- if (av.getWrapAlignment())
+ Integer idwidth = null;
+ if (onscreen
+ || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null)
{
- height = getWrappedHeight();
- if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
- {
- // TODO: JAL-244
- width = alignFrame.getWidth() - vscroll.getPreferredSize().width
- - alignFrame.getInsets().left
- - alignFrame.getInsets().right;
- }
- else
- {
- width = seqPanel.getWidth() + getVisibleIdWidth();
- }
-
- }
- else if (av.getShowAnnotation())
- {
- height += annotationPanel.adjustPanelHeight() + 3;
+ return (idPanel.getWidth() > 0 ? idPanel.getWidth()
+ : calculateIdWidth().width + 4);
}
+ return idwidth.intValue() + 4;
+ }
+ void makeAlignmentImage(int type, File file)
+ {
+ long progress = System.currentTimeMillis();
+ boolean 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);
+ }
try
{
-
- jalview.util.ImageMaker im;
- if (type == jalview.util.ImageMaker.PNG)
+ int maxwidth = av.getAlignment().getWidth();
+ if (av.hasHiddenColumns())
{
- 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());
+ 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())
{
- if (im.getGraphics() != null)
+ height = getWrappedHeight();
+ if (headless)
{
- printWrappedAlignment(im.getGraphics(), width, height, 0);
- im.writeImage();
+ // 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
+ else if (av.getShowAnnotation())
+ {
+ height += annotationPanel.adjustPanelHeight() + 3;
+ }
+
+ try
{
- if (im.getGraphics() != null)
+
+ jalview.util.ImageMaker im;
+ final String imageAction, imageTitle;
+ if (type == jalview.util.ImageMaker.PNG)
+ {
+ imageAction = "Create PNG image from alignment";
+ imageTitle = null;
+ }
+ else
+ {
+ imageAction = "Create EPS file from alignment";
+ imageTitle = alignFrame.getTitle();
+ }
+ im = new jalview.util.ImageMaker(this, type, imageAction, width,
+ height, file, imageTitle);
+ if (av.getWrapAlignment())
{
- printUnwrapped(im.getGraphics(), width, height, 0);
- im.writeImage();
+ if (im.getGraphics() != null)
+ {
+ printWrappedAlignment(im.getGraphics(), width, height, 0);
+ im.writeImage();
+ }
}
+ else
+ {
+ if (im.getGraphics() != null)
+ {
+ printUnwrapped(im.getGraphics(), width, height, 0);
+ im.writeImage();
+ }
+ }
+ } catch (OutOfMemoryError err)
+ {
+ // Be noisy here.
+ System.out.println("########################\n" + "OUT OF MEMORY "
+ + file + "\n" + "########################");
+ new OOMWarning("Creating Image for " + file, err);
+ // System.out.println("Create IMAGE: " + err);
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
}
- } catch (OutOfMemoryError err)
- {
- // Be noisy here.
- System.out.println("########################\n" + "OUT OF MEMORY "
- + file + "\n" + "########################");
- new OOMWarning("Creating Image for " + file, err);
- // System.out.println("Create IMAGE: " + err);
- } catch (Exception ex)
+ } finally
{
- ex.printStackTrace();
+ if (alignFrame != null && !headless)
+ {
+ alignFrame.setProgressBar("Export complete.", progress);
+ }
}
}
{
// /////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
- .getWidth(), g, gSize, f, fSize, sy;
+ 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));
out.println(jalview.io.HTMLOutput.getImageMapHTML());
{
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;
}
PaintRefresher.RemoveComponent(this);
if (av != null)
{
- jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager();
+ jalview.structure.StructureSelectionManager ssm = av
+ .getStructureSelectionManager();
ssm.removeStructureViewerListener(seqPanel, null);
ssm.removeSelectionListener(seqPanel);
- av.alignment = null;
+ av.setAlignment(null);
av = null;
}
else
*/
public void updateAnnotation()
{
- updateAnnotation(false);
+ updateAnnotation(false, false);
}
public void updateAnnotation(boolean applyGlobalSettings)
{
- // TODO: this should be merged with other annotation update stuff - that
- // sits on AlignViewport
- boolean updateCalcs = false;
- boolean conv = av.isShowGroupConservation();
- boolean cons = av.isShowGroupConsensus();
- boolean showprf = av.isShowSequenceLogo();
- boolean showConsHist = av.isShowConsensusHistogram();
- boolean normLogo = av.isNormaliseSequenceLogo();
-
- 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
+ updateAnnotation(applyGlobalSettings, false);
+ }
- 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);
- sg.setNormaliseSequenceLogo(normLogo);
- }
- 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();
+ public void updateAnnotation(boolean applyGlobalSettings,
+ boolean preserveNewGroupSettings)
+ {
+ av.updateGroupAnnotationSettings(applyGlobalSettings,
+ preserveNewGroupSettings);
adjustAnnotationHeight();
}
@Override
public AlignmentI getAlignment()
{
- return av.alignment;
+ return av.getAlignment();
}
/**
* get the name for this view
- * @return
+ *
+ * @return
*/
public String getViewName()
{
/**
* Make/Unmake this alignment panel the current input focus
+ *
* @param b
*/
public void setSelected(boolean b)
{
- try {
+ try
+ {
alignFrame.setSelected(b);
- } catch (Exception ex) {};
-
+ } catch (Exception ex)
+ {
+ }
+ ;
+
if (b)
{
alignFrame.setDisplayedView(this);
- }
+ }
}
@Override
{
return av.getStructureSelectionManager();
}
+
+ @Override
+ public void raiseOOMWarning(String string, OutOfMemoryError error)
+ {
+ new OOMWarning(string, error, this);
+ }
+
+ public FeatureRenderer cloneFeatureRenderer()
+ {
+
+ return new FeatureRenderer(this);
+ }
+
+ public void updateFeatureRenderer(FeatureRenderer fr)
+ {
+ fr.transferSettings(seqPanel.seqCanvas.getFeatureRenderer());
+ }
+
+ public void updateFeatureRendererFrom(FeatureRenderer fr)
+ {
+ if (seqPanel.seqCanvas.getFeatureRenderer() != null)
+ {
+ seqPanel.seqCanvas.getFeatureRenderer().transferSettings(fr);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff