*/
package jalview.gui;
+import java.awt.Canvas;
import java.awt.Color;
import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.awt.geom.AffineTransform;
-import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator;
import java.util.Locale;
-import java.util.concurrent.Callable;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JMenuItem;
import jalview.analysis.AlignSeq;
import jalview.analysis.AlignmentUtils;
-import jalview.bin.Console;
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.FormatAdapter;
-import jalview.io.NewickFile;
import jalview.util.Comparison;
import jalview.util.MessageManager;
import jalview.util.Platform;
-import jalview.ws.datamodel.alphafold.PAEContactMatrix;
/**
* The panel that holds the labels for alignment annotations, providing
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;
+
/**
* Creates a new AnnotationLabels object
*
*/
public AnnotationLabels(AlignmentPanel ap)
{
-
this.ap = ap;
av = ap.av;
ToolTipManager.sharedInstance().registerComponent(this);
ap.av.getAlignment().setAnnotationIndex(annotation, 0);
}
ap.refresh(true);
- return null;
});
}
consclipbrd.addActionListener(this);
pop.add(consclipbrd);
}
+
+ addColourOrFilterByOptions(ap, aa[selectedRow], pop);
+
if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP)
{
-
- final ContactMatrixI cm = av.getContactMatrix(aa[selectedRow]);
- if (cm != null)
+ 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)
+ {
+ JMenuItem item;
+ 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);
+ };
+ });
+ pop.add(item);
+ if (alignmentAnnotation.sequenceRef != null)
+ {
+ item = new JMenuItem(
+ MessageManager.getString("label.colour_by_annotation") + " ("
+ + MessageManager.getString("label.per_seq") + ")");
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- pop.addSeparator();
+ AnnotationColourChooser.displayFor(ap.av, ap, alignmentAnnotation,
+ true);
+ };
+ });
+ pop.add(item);
+ }
+ 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);
+ };
+ });
+ pop.add(item);
+ }
+
+ static void addContactMatrixOptions(final AlignmentPanel ap,
+ final AlignmentAnnotation alignmentAnnotation,
+ final JPopupMenu pop)
+ {
+
+ final ContactMatrixI cm = ap.av.getContactMatrix(alignmentAnnotation);
+ JMenuItem item;
+ if (cm != null)
+ {
+ pop.addSeparator();
- if (cm.hasTree())
+ 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;
+ chitem.setState(showGroups);
+ chitem.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- item = new JMenuItem("Show Tree for Matrix");
- item.addActionListener(new ActionListener()
- {
+ sel_row.setShowGroupsForContactMatrix(chitem.getState());
+ // so any annotation colour changes are propagated - though they
+ // probably won't be unless the annotation row colours are removed
+ // too!
+ ap.alignmentChanged();
+ }
+ });
+ pop.add(chitem);
+ }
+ if (cm.hasTree())
+ {
+ item = new JMenuItem(
+ MessageManager.getString("action.show_tree_for_matrix"));
+ item.setToolTipText(MessageManager
+ .getString("action.show_tree_for_matrix_tooltip"));
+ item.addActionListener(new ActionListener()
+ {
- @Override
- public void actionPerformed(ActionEvent e)
- {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
- ap.alignFrame.showContactMapTree(aa[selectedRow], cm);
+ ap.alignFrame.showContactMapTree(alignmentAnnotation, cm);
- }
- });
- pop.add(item);
}
- else
+ });
+ pop.add(item);
+ }
+ else
+ {
+ item = new JMenuItem(
+ MessageManager.getString("action.cluster_matrix"));
+ item.setToolTipText(
+ MessageManager.getString("action.cluster_matrix_tooltip"));
+ item.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
{
- item = new JMenuItem("Calculate Tree for Matrix");
- item.addActionListener(new ActionListener()
+ new Thread(new Runnable()
{
- // TODO - refactor to analysis background thread
@Override
- public void actionPerformed(ActionEvent e)
+ public void run()
{
- new Thread(new Runnable()
- {
- @Override
- public void run()
- {
- AlignmentAnnotation alan = aa[selectedRow];
- cm.setGroupSet(GroupSet.makeGroups(cm, 5f, true));
- ap.alignFrame.showContactMapTree(alan, cm);
- }
- }).start();
+ final long progBar;
+ 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);
+ ap.alignmentChanged();
+ ap.alignFrame.showContactMapTree(alignmentAnnotation, cm);
+ ap.alignFrame.setProgressBar(null, progBar);
}
- });
- pop.add(item);
-
+ }).start();
}
- // Show/Hide group shading on matrix view
- // Set/adjust threshold for grouping ?
- // colour alignment by this [type]
- // select/hide columns by this row
-
- }
+ });
+ pop.add(item);
}
}
- pop.show(this, evt.getX(), evt.getY());
}
/**
* @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);
+ }
- FontMetrics fm = g.getFontMetrics(g.getFont());
- g.setColor(Color.white);
- g.fillRect(0, 0, getWidth(), getHeight());
+ /**
+ * 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());
+ }
- 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;
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(Color.black);
+ g.setColor(aa[gg]._linecolour);
+ g.drawLine(x, y - graphExtras + 3,
+ x + fm.stringWidth(aa[gg].label),
+ y - graphExtras + 3);
+ }
+
+ 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()
git://source.jalview.org / jalview.git / blobdiff