import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
- import java.util.EnumSet;
import java.util.HashMap;
import java.util.Iterator;
import java.util.List;
if (avm == null)
return true;
- /*
- * // script to execute after all loading is completed one way or another String
- * groovyscript = m.get(Arg.GROOVY) == null ? null :
- * m.get(Arg.GROOVY).getValue(); String file = m.get(Arg.OPEN) == null ? null :
- * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
- * DataSourceType protocol = null;
- */
+ // set wrap scope here so it can be applied after structures are opened
+ boolean wrap = false;
+
if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
{
commandArgsProvided = true;
af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
format);
- // wrap alignment?
- boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
- null, "WRAP_ALIGNMENT", false);
- af.getCurrentView().setWrapAlignment(wrap);
-
// colour alignment?
String colour = ArgParser.getFromSubValArgOrPref(avm, av,
Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
false, false);
}
+ // wrap alignment? do this last for formatting reasons
+ wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv, null,
+ "WRAP_ALIGNMENT", false);
+ // af.setWrapFormat(wrap) is applied after structures are opened for
+ // annotation reasons
+
// store the AlignFrame for this id
afMap.put(id, af);
String sViewer = ArgParser.getFromSubValArgOrPref(avm,
Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null,
null, "jmol");
- ViewerType viewerType = null;
- if (!"none".equals(sViewer))
- {
- for (ViewerType v : EnumSet.allOf(ViewerType.class))
- {
- String name = v.name().toLowerCase(Locale.ROOT)
- .replaceAll(" ", "");
- if (sViewer.equals(name))
- {
- viewerType = v;
- break;
- }
- }
- }
+ ViewerType viewerType = ViewerType.getFromString(sViewer);
// TODO use ssFromStructure
StructureViewer sv = StructureChooser
}
}
+ if (wrap)
+ {
+ AlignFrame af = afMap.get(id);
+ if (af != null)
+ {
+ af.setWrapFormat(wrap, true);
+ }
+ }
+
/*
boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
if (doShading)
String val = av.getValue();
SubVals subVals = av.getSubVals();
String fileName = subVals.getContent();
+ boolean stdout = ArgParser.STDOUTFILENAME.equals(fileName);
File file = new File(fileName);
boolean overwrite = ArgParser.getFromSubValArgOrPref(avm,
Arg.OVERWRITE, subVals, null, "OVERWRITE_OUTPUT", false);
!Platform.isHeadless());
// if backups is not true then --overwrite must be specified
- if (file.exists() && !(overwrite || backups))
+ if (file.exists() && !(overwrite || backups || stdout))
{
Console.error("Won't overwrite file '" + fileName + "' without "
+ Arg.OVERWRITE.argString() + " or "
}
if (ff == null)
{
- StringBuilder validSB = new StringBuilder();
- for (String f : validFormats)
- {
- if (validSB.length() > 0)
- validSB.append(", ");
- validSB.append(f);
- FileFormatI tff = ffs.forName(f);
- validSB.append(" (");
- validSB.append(tff.getExtensions());
- validSB.append(")");
+ if (stdout)
+ {
+ ff = FileFormat.Fasta;
}
+ else
+ {
+ StringBuilder validSB = new StringBuilder();
+ for (String f : validFormats)
+ {
+ if (validSB.length() > 0)
+ validSB.append(", ");
+ validSB.append(f);
+ FileFormatI tff = ffs.forName(f);
+ validSB.append(" (");
+ validSB.append(tff.getExtensions());
+ validSB.append(")");
+ }
- Jalview.exit("No valid format specified for "
- + Arg.OUTPUT.argString() + ". Valid formats are "
- + validSB.toString() + ".", 1);
- // this return really shouldn't happen
- return false;
+ Jalview.exit("No valid format specified for "
+ + Arg.OUTPUT.argString() + ". Valid formats are "
+ + validSB.toString() + ".", 1);
+ // this return really shouldn't happen
+ return false;
+ }
}
String savedBackupsPreference = Cache
Console.info("Writing " + fileName);
- af.saveAlignment(fileName, ff);
+ af.saveAlignment(fileName, ff, stdout);
Console.debug("Returning backups to " + savedBackupsPreference);
if (savedBackupsPreference != null)
Cache.applicationProperties.put(BackupFiles.ENABLED,
import java.io.File;
import java.io.FileWriter;
import java.io.IOException;
+import java.io.OutputStreamWriter;
import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
// if (viewport.cursorMode)
// {
// alignPanel.seqPanel.insertNucAtCursor(false,"A");
- // //System.out.println("A");
+ // //jalview.bin.Console.outPrintln("A");
// }
// break;
/*
* case KeyEvent.VK_CLOSE_BRACKET: if (viewport.cursorMode) {
- * System.out.println("closing bracket"); } break;
+ * jalview.bin.Console.outPrintln("closing bracket"); } break;
*/
case KeyEvent.VK_DELETE:
case KeyEvent.VK_BACK_SPACE:
@Override
public void propertyChange(PropertyChangeEvent evt)
{
- // // System.out.println("Discoverer property change.");
+ // // jalview.bin.Console.outPrintln("Discoverer property
+ // change.");
// if (evt.getPropertyName().equals("services"))
{
SwingUtilities.invokeLater(new Runnable()
@Override
public void run()
{
- System.err.println(
+ jalview.bin.Console.errPrintln(
"Rebuild WS Menu for service change");
BuildWebServiceMenu();
}
public void internalFrameClosed(
javax.swing.event.InternalFrameEvent evt)
{
- // System.out.println("deregistering discoverer listener");
+ // jalview.bin.Console.outPrintln("deregistering discoverer listener");
Desktop.instance.removeJalviewPropertyChangeListener("services",
thisListener);
closeMenuItem_actionPerformed(true);
*/
public void saveAlignment(String file, FileFormatI format)
{
+ saveAlignment(file, format, false);
+ }
+
+ public void saveAlignment(String file, FileFormatI format, boolean stdout)
+ {
lastSaveSuccessful = true;
- lastFilenameSaved = file;
+ if (!stdout)
+ {
+ lastFilenameSaved = file;
+ }
lastFormatSaved = format;
if (FileFormat.Jalview.equals(format))
shortName = shortName
.substring(shortName.lastIndexOf(File.separatorChar) + 1);
}
+ // TODO deal with stdout=true
lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
shortName);
else
{
// create backupfiles object and get new temp filename destination
- boolean doBackup = BackupFiles.getEnabled();
+ boolean doBackup = BackupFiles.getEnabled() && !stdout;
BackupFiles backupfiles = null;
if (doBackup)
{
String tempFilePath = doBackup ? backupfiles.getTempFilePath()
: file;
Console.trace("ALIGNFRAME setting PrintWriter");
- PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
+ PrintWriter out = stdout
+ ? new PrintWriter(new OutputStreamWriter(System.out))
+ : new PrintWriter(new FileWriter(tempFilePath));
if (backupfiles != null)
{
}
out.print(output);
- Console.trace("ALIGNFRAME about to close file");
- out.close();
- Console.trace("ALIGNFRAME closed file");
- AlignFrame.this.setTitle(file);
- statusBar.setText(MessageManager.formatMessage(
- "label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format.getName() }));
+ out.flush();
+ if (!stdout)
+ {
+ Console.trace("ALIGNFRAME about to close file");
+ out.close();
+ Console.trace("ALIGNFRAME closed file");
+ }
+ AlignFrame.this.setTitle(stdout ? "STDOUT" : file);
+ if (stdout)
+ {
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_printed_to_stdout_in_format",
+ new Object[]
+ { format.getName() }));
+ }
+ else
+ {
+ statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_saved_to_file_in_format",
+ new Object[]
+ { fileName, format.getName() }));
+ }
lastSaveSuccessful = true;
} catch (IOException e)
{
} catch (Exception ex)
{
ex.printStackTrace();
- System.out.println("Exception whilst pasting: " + ex);
+ jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex);
// could be anything being pasted in here
}
} catch (Exception ex)
{
ex.printStackTrace();
- System.out.println("Exception whilst pasting: " + ex);
+ jalview.bin.Console.outPrintln("Exception whilst pasting: " + ex);
// could be anything being pasted in here
} catch (OutOfMemoryError oom)
{
@Override
public void wrapMenuItem_actionPerformed(ActionEvent e)
{
- scaleAbove.setVisible(wrapMenuItem.isSelected());
- scaleLeft.setVisible(wrapMenuItem.isSelected());
- scaleRight.setVisible(wrapMenuItem.isSelected());
- viewport.setWrapAlignment(wrapMenuItem.isSelected());
+ setWrapFormat(wrapMenuItem.isSelected(), false);
+ }
+
+ public void setWrapFormat(boolean b, boolean setMenuItem)
+ {
+ scaleAbove.setVisible(b);
+ scaleLeft.setVisible(b);
+ scaleRight.setVisible(b);
+ viewport.setWrapAlignment(b);
alignPanel.updateLayout();
+ if (setMenuItem)
+ {
+ wrapMenuItem.setSelected(b);
+ }
}
@Override
{
try
{
- System.err.println("Waiting for building menu to finish.");
+ jalview.bin.Console
+ .errPrintln("Waiting for building menu to finish.");
Thread.sleep(10);
} catch (Exception e)
{
final List<JMenuItem> legacyItems = new ArrayList<>();
try
{
- // System.err.println("Building ws menu again "
+ // jalview.bin.Console.errPrintln("Building ws menu again "
// + Thread.currentThread());
// TODO: add support for context dependent disabling of services based
// on
Desktop.instance);
if (pe != null)
{
- System.err.println("Associated file : "
+ jalview.bin.Console.errPrintln("Associated file : "
+ (fm[0].toString()) + " with "
+ toassoc.getDisplayId(true));
assocfiles++;
viewport.getAlignment()));
} catch (Exception ex)
{
- System.err.println(ex.getMessage());
+ jalview.bin.Console.errPrintln(ex.getMessage());
return;
}
}
console.runScript();
} catch (Exception ex)
{
- System.err.println((ex.toString()));
+ jalview.bin.Console.errPrintln((ex.toString()));
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.getString("label.couldnt_run_groovy_script"),
MessageManager.getString("label.groovy_support_failed"),
}
else
{
- System.err.println("Can't run Groovy script as console not found");
+ jalview.bin.Console
+ .errPrintln("Can't run Groovy script as console not found");
}
}
import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.bin.Jalview;
+ import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SearchResultsI;
Dimension r = null;
if (av.getIdWidth() < 0)
{
- int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
- int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
- int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
- r = calculateIdWidth(maxwidth);
+ r = calculateDefaultAlignmentIdWidth();
av.setIdWidth(r.width);
}
else
return r;
}
+ public Dimension calculateDefaultAlignmentIdWidth()
+ {
+ int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300);
+ int idWidth = Math.min(afwidth - 200, 2 * afwidth / 3);
+ int maxwidth = Math.max(IdwidthAdjuster.MIN_ID_WIDTH, idWidth);
+ return calculateIdWidth(-1, false, false);
+ }
+
/**
* Calculate the width of the alignment labels based on the displayed names
* and any bounds on label width set in preferences.
*/
protected Dimension calculateIdWidth(int maxwidth)
{
+ return calculateIdWidth(maxwidth, true, false);
+ }
+
+ public Dimension calculateIdWidth(int maxwidth,
+ boolean includeAnnotations, boolean visibleOnly)
+ {
Container c = new Container();
FontMetrics fm = c.getFontMetrics(
}
// Also check annotation label widths
- i = 0;
-
- if (al.getAlignmentAnnotation() != null)
+ if (includeAnnotations && al.getAlignmentAnnotation() != null)
{
- fm = c.getFontMetrics(getAlabels().getFont());
-
- while (i < al.getAlignmentAnnotation().length)
+ if (Jalview.isHeadlessMode())
{
- String label = al.getAlignmentAnnotation()[i].label;
- int stringWidth = fm.stringWidth(label);
+ AnnotationLabels aal = this.getAlabels();
+ int stringWidth = aal.drawLabels(null, false, idWidth, false, fm);
idWidth = Math.max(idWidth, stringWidth);
- i++;
+ }
+ else
+ {
+ fm = c.getFontMetrics(getAlabels().getFont());
+
+ for (i = 0; i < al.getAlignmentAnnotation().length; i++)
+ {
+ AlignmentAnnotation aa = al.getAlignmentAnnotation()[i];
+ if (visibleOnly && !aa.visible)
+ {
+ continue;
+ }
+ String label = aa.label;
+ int stringWidth = fm.stringWidth(label);
+ idWidth = Math.max(idWidth, stringWidth);
+ }
}
}
// this is called after loading new annotation onto alignment
if (alignFrame.getHeight() == 0)
{
- System.out.println("NEEDS FIXING");
+ jalview.bin.Console.outPrintln("NEEDS FIXING");
}
validateAnnotationDimensions(true);
addNotify();
// not be called directly by programs.
// I note that addNotify() is called in several areas of Jalview.
- int annotationHeight = getAnnotationPanel().adjustPanelHeight();
- annotationHeight = getAnnotationPanel()
- .adjustForAlignFrame(adjustPanelHeight, annotationHeight);
+ AnnotationPanel ap = getAnnotationPanel();
+ int annotationHeight = ap.adjustPanelHeight();
+ annotationHeight = ap.adjustForAlignFrame(adjustPanelHeight,
+ annotationHeight);
hscroll.addNotify();
- annotationScroller.setPreferredSize(
- new Dimension(annotationScroller.getWidth(), annotationHeight));
-
Dimension e = idPanel.getSize();
- alabels.setSize(new Dimension(e.width, annotationHeight));
+ int idWidth = e.width;
+ boolean manuallyAdjusted = this.getIdPanel().getIdCanvas()
+ .manuallyAdjusted();
+ annotationScroller.setPreferredSize(new Dimension(
+ manuallyAdjusted ? idWidth : annotationScroller.getWidth(),
+ annotationHeight));
+
+ alabels.setPreferredSize(new Dimension(idWidth, annotationHeight));
annotationSpaceFillerHolder.setPreferredSize(new Dimension(
- annotationSpaceFillerHolder.getWidth(), annotationHeight));
+ manuallyAdjusted ? idWidth
+ : annotationSpaceFillerHolder.getWidth(),
+ annotationHeight));
annotationScroller.validate();
annotationScroller.addNotify();
+ ap.validate();
}
/**
boolean wrap = av.getWrapAlignment();
ViewportRanges ranges = av.getRanges();
ranges.setStartSeq(0);
- scalePanelHolder.setVisible(!wrap);
+ // scalePanelHolder.setVisible(!wrap);
hscroll.setVisible(!wrap);
- idwidthAdjuster.setVisible(!wrap);
+ // Allow idPanel width adjustment in wrap mode
+ idwidthAdjuster.setVisible(true);
if (wrap)
{
}
}
- idSpaceFillerPanel1.setVisible(!wrap);
+ // idSpaceFillerPanel1.setVisible(!wrap);
repaint();
}
public void paintComponent(Graphics g)
{
invalidate(); // needed so that the id width adjuster works correctly
-
Dimension d = getIdPanel().getIdCanvas().getPreferredSize();
- idPanelHolder.setPreferredSize(d);
- hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12));
+ int idWidth = d.width;
+
+ // check wrapped alignment as at least 1 residue width
+ if (av.getWrapAlignment())
+ {
+ SeqCanvas sc = this.getSeqPanel().seqCanvas;
+ if (sc != null && sc.getWidth() < sc.getMinimumWrappedCanvasWidth())
+ {
+ // need to make some adjustments
+ idWidth -= (sc.getMinimumWrappedCanvasWidth() - sc.getWidth());
+ av.setIdWidth(idWidth);
+ av.getAlignPanel().getIdPanel().getIdCanvas()
+ .setManuallyAdjusted(true);
+
+ validateAnnotationDimensions(false);
+ }
+ }
+
+ idPanelHolder.setPreferredSize(new Dimension(idWidth, d.height));
+ hscrollFillerPanel.setPreferredSize(new Dimension(idWidth, 12));
validate(); // needed so that the id width adjuster works correctly
}
int w = getIdPanel().getWidth();
+ w = this.calculateIdWidth(-1, true, true).width;
return (w > 0 ? w : calculateIdWidth().width);
}
- void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer) throws ImageOutputException
+ void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer)
+ throws ImageOutputException
{
makeAlignmentImage(type, file, renderer,
BitmapImageSizing.nullBitmapImageSizing());
final int borderBottomOffset = 5;
AlignmentDimension aDimension = getAlignmentDimension();
+
// todo use a lambda function in place of callback here?
ImageWriterI writer = new ImageWriterI()
{
}
- public void makePNGImageMap(File imgMapFile, String imageName) throws ImageOutputException
+ public void makePNGImageMap(File imgMapFile, String imageName)
+ throws ImageOutputException
{
// /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS
// ////////////////////////////////////////////
} catch (Exception ex)
{
- throw new ImageOutputException("couldn't write ImageMap due to unexpected error",ex);
+ throw new ImageOutputException(
+ "couldn't write ImageMap due to unexpected error", ex);
}
} // /////////END OF IMAGE MAP
{
int seqPanelWidth = getSeqPanel().seqCanvas.getWidth();
- if (System.getProperty("java.awt.headless") != null
- && System.getProperty("java.awt.headless").equals("true"))
+ if (Jalview.isHeadlessMode())
{
seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth()
- vscroll.getPreferredSize().width
*/
package jalview.gui;
+ import java.awt.Canvas;
import java.awt.Color;
import java.awt.Cursor;
import java.awt.Dimension;
import jalview.analysis.AlignSeq;
import jalview.analysis.AlignmentUtils;
+ import jalview.bin.Cache;
+ import jalview.bin.Jalview;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
/**
* height in pixels for allowing height adjuster to be active
*/
- private static int HEIGHT_ADJUSTER_HEIGHT = 10;
+ public static int HEIGHT_ADJUSTER_HEIGHT = 10;
private static final Font font = new Font("Arial", Font.PLAIN, 11);
private static final String COPYCONS_SEQ = MessageManager
.getString("label.copy_consensus_sequence");
+ private static final String ADJUST_ANNOTATION_LABELS_WIDTH_PREF = "ADJUST_ANNOTATION_LABELS_WIDTH";
+
private final boolean debugRedraw = false;
private AlignmentPanel ap;
private boolean resizePanel = false;
+ private int annotationIdWidth = -1;
+
+ public static final String RESIZE_MARGINS_MARK_PREF = "RESIZE_MARGINS_MARK";
+
/**
* Creates a new AnnotationLabels object
*
*/
public AnnotationLabels(AlignmentPanel ap)
{
-
this.ap = ap;
av = ap.av;
ToolTipManager.sharedInstance().registerComponent(this);
pop.add(consclipbrd);
}
- addColourOrFilterByOptions(ap,aa[selectedRow],pop);
-
+ addColourOrFilterByOptions(ap, aa[selectedRow], pop);
+
if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP)
{
- addContactMatrixOptions(ap,aa[selectedRow],pop);
- // Set/adjust threshold for grouping ?
- // colour alignment by this [type]
- // select/hide columns by this row
-
- }
+ addContactMatrixOptions(ap, aa[selectedRow], pop);
+ // Set/adjust threshold for grouping ?
+ // colour alignment by this [type]
+ // select/hide columns by this row
+
}
-
+ }
+
pop.show(this, evt.getX(), evt.getY());
}
static void addColourOrFilterByOptions(final AlignmentPanel ap,
- final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop)
+ final AlignmentAnnotation alignmentAnnotation,
+ final JPopupMenu pop)
{
JMenuItem item;
- item = new JMenuItem(MessageManager.getString("label.colour_by_annotation"));
+ item = new JMenuItem(
+ MessageManager.getString("label.colour_by_annotation"));
item.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
- AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,false);
+ AnnotationColourChooser.displayFor(ap.av, ap, alignmentAnnotation,
+ false);
};
});
pop.add(item);
- if (alignmentAnnotation.sequenceRef!=null)
+ if (alignmentAnnotation.sequenceRef != null)
{
- item = new JMenuItem(MessageManager.getString("label.colour_by_annotation")+" ("+MessageManager.getString("label.per_seq")+")");
+ item = new JMenuItem(
+ MessageManager.getString("label.colour_by_annotation") + " ("
+ + MessageManager.getString("label.per_seq") + ")");
item.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- AnnotationColourChooser.displayFor(ap.av, ap,alignmentAnnotation,true);
+ AnnotationColourChooser.displayFor(ap.av, ap, alignmentAnnotation,
+ true);
};
});
pop.add(item);
}
- item = new JMenuItem(MessageManager.getString("action.select_by_annotation"));
+ item = new JMenuItem(
+ MessageManager.getString("action.select_by_annotation"));
item.addActionListener(new ActionListener()
{
-
+
@Override
public void actionPerformed(ActionEvent e)
{
- AnnotationColumnChooser.displayFor(ap.av,ap,alignmentAnnotation);
+ AnnotationColumnChooser.displayFor(ap.av, ap, alignmentAnnotation);
};
});
pop.add(item);
}
+
static void addContactMatrixOptions(final AlignmentPanel ap,
- final AlignmentAnnotation alignmentAnnotation, final JPopupMenu pop)
+ final AlignmentAnnotation alignmentAnnotation,
+ final JPopupMenu pop)
{
-
+
final ContactMatrixI cm = ap.av.getContactMatrix(alignmentAnnotation);
JMenuItem item;
if (cm != null)
if (cm.hasGroups())
{
- JCheckBoxMenuItem chitem = new JCheckBoxMenuItem(MessageManager.getString("action.show_groups_on_matrix"));
- chitem.setToolTipText(MessageManager.getString("action.show_groups_on_matrix_tooltip"));
- boolean showGroups = alignmentAnnotation.isShowGroupsForContactMatrix();
- final AlignmentAnnotation sel_row=alignmentAnnotation;
+ JCheckBoxMenuItem chitem = new JCheckBoxMenuItem(
+ MessageManager.getString("action.show_groups_on_matrix"));
+ chitem.setToolTipText(MessageManager
+ .getString("action.show_groups_on_matrix_tooltip"));
+ boolean showGroups = alignmentAnnotation
+ .isShowGroupsForContactMatrix();
+ final AlignmentAnnotation sel_row = alignmentAnnotation;
chitem.setState(showGroups);
chitem.addActionListener(new ActionListener()
{
}
if (cm.hasTree())
{
- item = new JMenuItem(MessageManager.getString("action.show_tree_for_matrix"));
- item.setToolTipText(MessageManager.getString("action.show_tree_for_matrix_tooltip"));
+ item = new JMenuItem(
+ MessageManager.getString("action.show_tree_for_matrix"));
+ item.setToolTipText(MessageManager
+ .getString("action.show_tree_for_matrix_tooltip"));
item.addActionListener(new ActionListener()
{
}
else
{
- item = new JMenuItem(MessageManager.getString("action.cluster_matrix"));
- item.setToolTipText(MessageManager.getString("action.cluster_matrix_tooltip"));
+ item = new JMenuItem(
+ MessageManager.getString("action.cluster_matrix"));
+ item.setToolTipText(
+ MessageManager.getString("action.cluster_matrix_tooltip"));
item.addActionListener(new ActionListener()
{
@Override
public void run()
{
final long progBar;
- ap.alignFrame.setProgressBar(MessageManager.formatMessage("action.clustering_matrix_for",cm.getAnnotDescr(),5f), progBar = System.currentTimeMillis());
+ ap.alignFrame.setProgressBar(
+ MessageManager.formatMessage(
+ "action.clustering_matrix_for",
+ cm.getAnnotDescr(), 5f),
+ progBar = System.currentTimeMillis());
cm.setGroupSet(GroupSet.makeGroups(cm, true));
cm.randomlyReColourGroups();
cm.transferGroupColorsTo(alignmentAnnotation);
}
drawComponent(g2, true, width);
-
}
/**
* @param width
* Width for scaling labels
*/
- public void drawComponent(Graphics g, boolean clip, int width)
+ public void drawComponent(Graphics g, boolean clip, int givenWidth)
{
- if (av.getFont().getSize() < 10)
+ int width = givenWidth;
+ IdwidthAdjuster iwa = null;
+ if (ap != null)
{
- g.setFont(font);
+ iwa = ap.idwidthAdjuster;
+ if ((Cache.getDefault(ADJUST_ANNOTATION_LABELS_WIDTH_PREF, true)
+ || Jalview.isHeadlessMode()))
+ {
+ Graphics2D g2d = (Graphics2D) g;
+ Graphics dummy = g2d.create();
+ int newAnnotationIdWidth = drawLabels(dummy, clip, width, false,
+ null);
+ dummy.dispose();
+ Dimension d = ap.calculateDefaultAlignmentIdWidth();
+ int alignmentIdWidth = d.width;
+ if (iwa != null && !iwa.manuallyAdjusted())
+ {
+ // If no manual adjustment to ID column with has been made then adjust
+ // width match widest of alignment or annotation id widths
+ boolean allowShrink = Cache.getDefault("ALLOW_SHRINK_ID_WIDTH",
+ false);
+ width = Math.max(alignmentIdWidth, newAnnotationIdWidth);
+ if (clip && width < givenWidth && !allowShrink)
+ {
+ width = givenWidth;
+ }
+ }
+ else if (newAnnotationIdWidth != annotationIdWidth
+ && newAnnotationIdWidth > givenWidth
+ && newAnnotationIdWidth > alignmentIdWidth)
+ {
+ // otherwise if the annotation id width has become larger than the
+ // current id width, increase
+ width = newAnnotationIdWidth;
+ annotationIdWidth = newAnnotationIdWidth;
+ }
+ // set the width if it's changed
+ if (width != ap.av.getIdWidth())
+ {
+ iwa.setWidth(width);
+ }
+ }
}
else
{
- g.setFont(av.getFont());
+ int newAnnotationIdWidth = drawLabels(g, clip, width, false, null);
+ width = Math.max(newAnnotationIdWidth, givenWidth);
+ }
+ drawLabels(g, clip, width, true, null);
+ }
+
+ /**
+ * Render the full set of annotation Labels for the alignment at the given
+ * cursor. If actuallyDraw is false or g is null then no actual drawing will
+ * occur, but the widest label width will be returned. If g is null then
+ * fmetrics must be supplied.
+ *
+ * Returns the width of the annotation labels.
+ *
+ * @param g
+ * Graphics2D instance (needed for font scaling)
+ * @param clip
+ * - true indicates that only current visible area needs to be
+ * rendered
+ * @param width
+ * Width for scaling labels
+ * @param fmetrics
+ * FontMetrics if Graphics object g is null
+ */
+ public int drawLabels(Graphics g0, boolean clip, int width,
+ boolean actuallyDraw, FontMetrics fmetrics)
+ {
+ if (clip)
+ {
+ clip = Cache.getDefault("MOVE_SEQUENCE_ID_WITH_VISIBLE_ANNOTATIONS",
+ true);
+ }
+ Graphics g = null;
+ // create a dummy Graphics object if not drawing and one is supplied
+ if (g0 != null)
+ {
+ if (!actuallyDraw)
+ {
+ Graphics2D g2d = (Graphics2D) g0;
+ g = g2d.create();
+ }
+ else
+ {
+ g = g0;
+ }
}
+ int actualWidth = 0;
+ if (g != null)
+ {
+ if (av.getFont().getSize() < 10)
+ {
+ g.setFont(font);
+ }
+ else
+ {
+ g.setFont(av.getFont());
+ }
+ }
+
+ FontMetrics fm = fmetrics == null ? g.getFontMetrics(g.getFont())
+ : fmetrics;
+ if (actuallyDraw)
+ {
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getWidth(), getHeight());
+
+ if (!Cache.getDefault(RESIZE_MARGINS_MARK_PREF, false)
+ && !av.getWrapAlignment())
+ {
+ g.setColor(Color.LIGHT_GRAY);
+ g.drawLine(0, HEIGHT_ADJUSTER_HEIGHT / 4, HEIGHT_ADJUSTER_WIDTH / 4,
+ HEIGHT_ADJUSTER_HEIGHT / 4);
+ g.drawLine(0, 3 * HEIGHT_ADJUSTER_HEIGHT / 4,
+ HEIGHT_ADJUSTER_WIDTH / 4, 3 * HEIGHT_ADJUSTER_HEIGHT / 4);
- FontMetrics fm = g.getFontMetrics(g.getFont());
- g.setColor(Color.white);
- g.fillRect(0, 0, getWidth(), getHeight());
+ }
+ }
- g.translate(0, getScrollOffset());
- g.setColor(Color.black);
+ if (actuallyDraw)
+ {
+ g.translate(0, getScrollOffset());
+ g.setColor(Color.black);
+ }
SequenceI lastSeqRef = null;
String lastLabel = null;
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
- int fontHeight = g.getFont().getSize();
+ int fontHeight = g != null ? g.getFont().getSize()
+ : fm.getFont().getSize();
int y = 0;
int x = 0;
int graphExtras = 0;
int offset = 0;
- Font baseFont = g.getFont();
+ Font baseFont = g != null ? g.getFont() : fm.getFont();
FontMetrics baseMetrics = fm;
int ofontH = fontHeight;
int sOffset = 0;
{
if (debugRedraw)
{
- System.out.println("before vis: " + i);
+ jalview.bin.Console.outPrintln("before vis: " + i);
}
before = true;
}
{
if (debugRedraw)
{
- System.out.println(
+ jalview.bin.Console.outPrintln(
"Scroll offset: " + sOffset + " after vis: " + i);
}
after = true;
continue;
}
}
- g.setColor(Color.black);
-
+ if (actuallyDraw && g != null)
+ {
+ g.setColor(Color.black);
+ }
offset = -aa[i].height / 2;
if (aa[i].hasText)
vertBar = true;
}
}
- x = width - fm.stringWidth(label) - 3;
+
+ int labelWidth = fm.stringWidth(label) + 3;
+ x = width - labelWidth;
if (aa[i].graphGroup > -1)
{
s = ((float) fontHeight) / (float) ofontH;
Font f = baseFont
.deriveFont(AffineTransform.getScaleInstance(s, s));
- g.setFont(f);
- fm = g.getFontMetrics();
- graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
- / 2;
+ Canvas c = new Canvas();
+ fm = c.getFontMetrics(f);
+ if (actuallyDraw && g != null)
+ {
+ g.setFont(f);
+ // fm = g.getFontMetrics();
+ graphExtras = (aa[i].height
+ - (groupSize * (fontHeight + 8))) / 2;
+ }
}
}
if (visible)
{
if (aa[gg].graphGroup == aa[i].graphGroup)
{
- x = width - fm.stringWidth(aa[gg].label) - 3;
- g.drawString(aa[gg].label, x, y - graphExtras);
-
- if (aa[gg]._linecolour != null)
+ labelWidth = fm.stringWidth(aa[gg].label) + 3;
+ x = width - labelWidth;
+ if (actuallyDraw && g != null)
{
+ g.drawString(aa[gg].label, x, y - graphExtras);
- g.setColor(aa[gg]._linecolour);
- g.drawLine(x, y - graphExtras + 3,
- x + fm.stringWidth(aa[gg].label),
- y - graphExtras + 3);
- }
+ if (aa[gg]._linecolour != null)
+ {
+
+ g.setColor(aa[gg]._linecolour);
+ g.drawLine(x, y - graphExtras + 3,
+ x + fm.stringWidth(aa[gg].label),
+ y - graphExtras + 3);
+ }
- g.setColor(Color.black);
+ g.setColor(Color.black);
+ }
graphExtras += fontHeight + 8;
}
}
}
- g.setFont(baseFont);
+ if (actuallyDraw && g != null)
+ {
+ g.setFont(baseFont);
+ }
fm = baseMetrics;
fontHeight = ofontH;
}
else
{
- if (vertBar)
+ if (actuallyDraw && g != null)
{
- g.drawLine(width - 3, y + offset - fontHeight, width - 3,
- (int) (y - 1.5 * aa[i].height - offset - fontHeight));
- // g.drawLine(20, y + offset, x - 20, y + offset);
+ if (vertBar)
+ {
+ g.drawLine(width - 3, y + offset - fontHeight, width - 3,
+ (int) (y - 1.5 * aa[i].height - offset - fontHeight));
+ // g.drawLine(20, y + offset, x - 20, y + offset);
+ }
+ g.drawString(label, x, y + offset);
}
- g.drawString(label, x, y + offset);
}
lastSeqRef = aa[i].sequenceRef;
+
+ if (labelWidth > actualWidth)
+ {
+ actualWidth = labelWidth;
+ }
}
}
if (!resizePanel && dragEvent != null && aa != null)
{
- g.setColor(Color.lightGray);
- g.drawString(
- (aa[selectedRow].sequenceRef == null ? ""
- : aa[selectedRow].sequenceRef.getName())
- + aa[selectedRow].label,
- dragEvent.getX(), dragEvent.getY() - getScrollOffset());
+ if (actuallyDraw && g != null)
+ {
+ g.setColor(Color.lightGray);
+ g.drawString(
+ (aa[selectedRow].sequenceRef == null ? ""
+ : aa[selectedRow].sequenceRef.getName())
+ + aa[selectedRow].label,
+ dragEvent.getX(), dragEvent.getY() - getScrollOffset());
+ }
}
if (!av.getWrapAlignment() && ((aa == null) || (aa.length < 1)))
{
- g.drawString(MessageManager.getString("label.right_click"), 2, 8);
- g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
- 18);
+ if (actuallyDraw && g != null)
+ {
+ g.drawString(MessageManager.getString("label.right_click"), 2, 8);
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+ 18);
+ }
}
+
+ return actualWidth;
}
public int getScrollOffset()
}
}
- // System.err.println(">>> FastPaint to " + transX + " " + transY + " "
+ // jalview.bin.Console.errPrintln(">>> FastPaint to " + transX + " " + transY + " "
// + horizontal + " " + vertical + " " + startRes + " " + endRes
// + " " + startSeq + " " + endSeq);
// Call repaint on alignment panel so that repaints from other alignment
// panel components can be aggregated. Otherwise performance of the
// overview window and others may be adversely affected.
- // System.out.println("SeqCanvas fastPaint() repaint() request...");
+ // jalview.bin.Console.outPrintln("SeqCanvas fastPaint() repaint() request...");
av.getAlignPanel().repaint();
} finally
{
labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
return (canvasWidth - labelWidthEast - labelWidthWest) / charWidth;
+ }
+
+ public int getMinimumWrappedCanvasWidth()
+ {
+ int charWidth = av.getCharWidth();
+ FontMetrics fm = getFontMetrics(av.getFont());
+ int labelWidth = 0;
+ if (av.getScaleRightWrapped() || av.getScaleLeftWrapped())
+ {
+ labelWidth = getLabelWidth(fm);
+ }
+ labelWidthEast = av.getScaleRightWrapped() ? labelWidth : 0;
+ labelWidthWest = av.getScaleLeftWrapped() ? labelWidth : 0;
+ return labelWidthEast + labelWidthWest + charWidth;
}
/**
public void propertyChange(PropertyChangeEvent evt)
{
String eventName = evt.getPropertyName();
- // System.err.println(">>SeqCanvas propertyChange " + eventName);
+ // jalview.bin.Console.errPrintln(">>SeqCanvas propertyChange " + eventName);
if (eventName.equals(SequenceGroup.SEQ_GROUP_CHANGED))
{
fastPaint = true;
else if (eventName.equals(ViewportRanges.MOVE_VIEWPORT))
{
fastPaint = false;
- // System.err.println("!!!! fastPaint false from MOVE_VIEWPORT");
+ // jalview.bin.Console.errPrintln("!!!! fastPaint false from MOVE_VIEWPORT");
repaint();
return;
}
import jalview.gui.structurechooser.StructureChooserQuerySource;
import jalview.gui.structurechooser.ThreeDBStructureChooserQuerySource;
import jalview.io.DataSourceType;
- import jalview.io.FileFormatException;
import jalview.io.JalviewFileChooser;
import jalview.io.JalviewFileView;
import jalview.jbgui.FilterOption;
import jalview.ws.DBRefFetcher;
import jalview.ws.DBRefFetcher.FetchFinishedListenerI;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
- import jalview.ws.dbsources.EBIAlfaFold;
import jalview.ws.seqfetcher.DbSourceProxy;
import jalview.ws.sifts.SiftsSettings;
// for moment, it will work fine as is because it is self-contained
String searchTerm = text.toLowerCase(Locale.ROOT);
searchTerm = searchTerm.split(":")[0];
- // System.out.println(">>>>> search term : " + searchTerm);
+ // jalview.bin.Console.outPrintln(">>>>> search term : " + searchTerm);
List<FTSDataColumnI> wantedFields = new ArrayList<>();
FTSRestRequest pdbRequest = new FTSRestRequest();
pdbRequest.setAllowEmptySeq(false);
sc.mainFrame.dispose();
if (showRefAnnotations)
+ {
showReferenceAnnotationsForSequence(ap.alignFrame, seq);
+ }
return sv;
}
git://source.jalview.org / jalview.git / commitdiff