/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
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);
+ 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;
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 (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"))
{
- // TODO: JAL-244
+ // 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(true);
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;
}
jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager();
ssm.removeStructureViewerListener(seqPanel, null);
ssm.removeSelectionListener(seqPanel);
- av.alignment = null;
+ 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());
+ Vector gr = av.getAlignment().getGroups(); // OrderedBy(av.getAlignment().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;
}
}
// 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)
@Override
public AlignmentI getAlignment()
{
- return av.alignment;
+ return av.getAlignment();
}
/**
{
return av.getStructureSelectionManager();
}
+
+ @Override
+ public void raiseOOMWarning(String string, OutOfMemoryError error)
+ {
+ new OOMWarning(string, error, this);
+ }
}
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
epsRendering.addItem("Text");
epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
"Prompt each time"));
-
+ autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
+ userIdWidth.setEnabled(autoIdWidth.isSelected());
+ userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
+ Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
+ userIdWidth.setText(wi == null ? "" : wi.toString());
blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
Boolean.toString(modellerOutput.isSelected()));
jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+ Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
+ Boolean.toString(autoIdWidth.isSelected()));
+ userIdWidth_actionPerformed();
+ Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
+ userIdWidth.getText());
+
Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
Boolean.toString(autoCalculateConsCheck.isSelected()));
Cache.applicationProperties.setProperty("SORT_BY_TREE",
maxColour.repaint();
}
+ @Override
+ protected void userIdWidth_actionPerformed()
+ {
+ try
+ {
+ String val = userIdWidth.getText().trim();
+ if (val.length() > 0)
+ {
+ Integer iw = Integer.parseInt(val);
+ if (iw.intValue() < 12)
+ {
+ throw new NumberFormatException();
+ }
+ userIdWidth.setText(iw.toString());
+ }
+ } catch (NumberFormatException x)
+ {
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ "The user defined width for the\nannotation and sequence ID columns\nin exported figures must be\nat least 12 pixels wide.",
+ "Invalid ID Column width",
+ JOptionPane.WARNING_MESSAGE);
+ userIdWidth.setText("");
+ }
+ }
+
+ @Override
+ protected void autoIdWidth_actionPerformed()
+ {
+ userIdWidth.setEnabled(!autoIdWidth.isSelected());
+ userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
+ }
+
}
/*
* Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
JLabel epsLabel = new JLabel();
protected JComboBox epsRendering = new JComboBox();
+
+ protected JLabel userIdWidthlabel = new JLabel();
+ protected JCheckBox autoIdWidth = new JCheckBox();
+ protected JTextField userIdWidth = new JTextField();
+
JLabel jLabel1 = new JLabel();
sortByTree.setText("Sort With New Tree");
sortByTree.setToolTipText("When selected, any trees calculated or loaded onto the alignment will automatically sort the alignment.");
sortByTree.setBounds(new Rectangle(22, 136, 168, 23));
+
+ autoIdWidth.setFont(JvSwingUtils.getLabelFont());
+ autoIdWidth.setText("Automatically set ID width");
+ autoIdWidth.setToolTipText("<html>"+JvSwingUtils.wrapTooltip("Adjusts the width of the generated EPS or PNG file to ensure even the longest sequence ID or annotation label is displayed")+"</html>");
+ autoIdWidth.setBounds(new Rectangle(228, 96,188,23));
+ autoIdWidth.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ autoIdWidth_actionPerformed();
+ }
+ });
+ userIdWidthlabel.setFont(JvSwingUtils.getLabelFont());
+ userIdWidthlabel.setText("Figure ID column width");
+ userIdWidth
+ .setToolTipText("<html>"+JvSwingUtils
+ .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")+"</html>");
+ userIdWidthlabel
+ .setToolTipText("<html>"+JvSwingUtils
+ .wrapTooltip("Manually specify the width of the left hand column where sequence IDs and annotation labels will be rendered in exported alignment figures. This setting will be ignored if 'Automatically set ID width' is set")+"</html>");
+ userIdWidthlabel.setBounds(new Rectangle(236, 120,168,23));
+ userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
+ userIdWidth.setText("");
+ userIdWidth.setBounds(new Rectangle(232,144,84,23));
+ userIdWidth.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ userIdWidth_actionPerformed();
+ }
+ });
modellerOutput.setFont(JvSwingUtils.getLabelFont());
modellerOutput.setText("Use Modeller Output");
modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+
dasPanel.setLayout(borderLayout4);
wsPanel.setLayout(borderLayout5);
wrap.setFont(JvSwingUtils.getLabelFont());
jPanel11.add(pfamjv);
jPanel11.add(pileupjv);
jPanel11.add(pirjv);
+ exportTab.add(autoIdWidth);
+ exportTab.add(userIdWidth);
+ exportTab.add(userIdWidthlabel);
exportTab.add(modellerOutput);
tabbedPane.add(calcTab, "Editing");
calcTab.add(autoCalculateConsCheck);
exportTab.add(jPanel11);
}
+ protected void autoIdWidth_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
+ protected void userIdWidth_actionPerformed()
+ {
+ // TODO Auto-generated method stub
+
+ }
+
protected void maxColour_actionPerformed()
{
// TODO Auto-generated method stub
git://source.jalview.org / jalview.git / commitdiff