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;
/**
* Calculates the width of the alignment labels based on the displayed names
- * and any bounds on label width set in preferences. The calculated width is
- * also set as a property of the viewport.
+ * and any bounds on label width set in preferences.
+ *
+ * The calculated width is set as a property of the viewport and the layout is
+ * updated.
*
* @return Dimension giving the maximum width of the alignment label panel
* that should be used.
public Dimension calculateDefaultAlignmentIdWidth()
{
+ return calculateIdWidth(-1, false, false);
+ }
+ /**
+ * pre 2.11.3 Id width calculation - used when importing old projects only
+ * @return
+ */
+ public int getLegacyIdWidth()
+ {
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);
+ Dimension w = calculateIdWidthOrLegacy(true, maxwidth, false, false);
+ return w.width;
}
/**
* Calculate the width of the alignment labels based on the displayed names
- * and any bounds on label width set in preferences.
+ * and any bounds on label width set in preferences. Also includes annotations
+ * not actually visible.
+ *
+ * FIXME JAL-244 JAL-4091 - doesn't include sequence associated annotation
+ * label decorators and only called during tests
*
* @param maxwidth
* -1 or maximum width allowed for IdWidth
*/
protected Dimension calculateIdWidth(int maxwidth)
{
+ return calculateIdWidth(maxwidth, true, false);
+ }
+ /**
+ * 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
+ * @param includeAnnotations - when true includes width of any additional marks in annotation id panel
+ * @param visibleOnly - when true, ignore label widths for hidden annotation rows
+ * @return Dimension giving the maximum width of the alignment label panel
+ * that should be used.
+ */
+ public Dimension calculateIdWidth(int maxwidth,
+ boolean includeAnnotations, boolean visibleOnly)
+ {
+ return calculateIdWidthOrLegacy(false, maxwidth, includeAnnotations, visibleOnly);
+ }
+
+ /**
+ * legacy mode or post 2.11.3 ID width calculation
+ * @param legacy - uses annotation labels, not rendered label width (excludes additional decorators)
+ * @param maxwidth
+ * @param includeAnnotations
+ * @param visibleOnly
+ * @return
+ */
+ private Dimension calculateIdWidthOrLegacy(boolean legacy, 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 (!legacy || Jalview.isHeadlessMode())
{
- String label = al.getAlignmentAnnotation()[i].label;
- int stringWidth = fm.stringWidth(label);
+ AnnotationLabels aal = getAlabels();
+ int stringWidth = aal.drawLabels(null, false, idWidth, false, false,
+ fm, !visibleOnly);
idWidth = Math.max(idWidth, stringWidth);
- i++;
+ }
+ else
+ {
+ 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.error("adjustAnnotationHeight called with zero height alignment window");
}
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()
+ .isManuallyAdjusted();
+ 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
Graphics idGraphics, Graphics alignmentGraphics)
throws PrinterException
{
- final int idWidth = getVisibleIdWidth(false);
-
+ final int idWidth, idWidthForGui;
+ // otherwise calculate it
+ idWidth = getVisibleIdWidth(false);
+// if (getIdPanel()!=null && getIdPanel().getWidth()>0)
+// {
+// // use the current IdPanel's width, if its set and non-zero
+// idWidthForGui = getIdPanel().getWidth();
+// } else {
+// idWidthForGui=0;
+// }
/*
* Get the horizontal offset to where we draw the sequences.
* This is idWidth if using a single Graphics context, else zero.
}
final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3;
+ alignmentGraphics.setColor(Color.white);
+ alignmentGraphics.fillRect(0, 0, pageWidth, pageHeight+scaleHeight);
+
/*
* draw the Scale at horizontal offset, then reset to top left (0, 0)
*/
IdCanvas idCanvas = getIdPanel().getIdCanvas();
List<SequenceI> selection = av.getSelectionGroup() == null ? null
: av.getSelectionGroup().getSequences(null);
+
idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1,
- selection);
+ selection, false,idWidth);
idGraphics.setFont(av.getFont());
idGraphics.translate(0, -scaleHeight);
int offset = getAlabels().getScrollOffset();
idGraphics.translate(0, -offset);
idGraphics.translate(0, alignmentDrawnHeight);
- getAlabels().drawComponent(idGraphics, idWidth);
+ getAlabels().drawComponentNotGUI(idGraphics, idWidth);
idGraphics.translate(0, -alignmentDrawnHeight);
/*
* draw sequence ids and annotation labels (if shown)
*/
IdCanvas idCanvas = getIdPanel().getIdCanvas();
- idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight);
+ idCanvas.drawIdsWrappedNoGUI((Graphics2D) g, av, 0, totalHeight);
g.translate(idWidth, 0);
// see if rendering offscreen - check preferences and calc width accordingly
if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false))
{
- return calculateIdWidth(-1).width;
+ return calculateIdWidth(-1,true,true).width;
}
Integer idwidth = onscreen ? null
: Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH");
}
int w = getIdPanel().getWidth();
+ w = calculateIdWidth(-1, true, true).width;
return (w > 0 ? w : calculateIdWidth().width);
}
throws ImageOutputException
{
makeAlignmentImage(type, file, renderer,
- BitmapImageSizing.nullBitmapImageSizing());
+ BitmapImageSizing.defaultBitmapImageSizing());
}
/**
final int borderBottomOffset = 5;
AlignmentDimension aDimension = getAlignmentDimension();
+
// todo use a lambda function in place of callback here?
ImageWriterI writer = new ImageWriterI()
{
{
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
overviewPanel = null;
}
}
-
}
git://source.jalview.org / jalview.git / blobdiff