X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=8e7c7455cacc5a4bd5800cc1ecb95f5f149d2a5d;hb=bc1a3842b31a35a7794f4afec4911ad421c7c3e4;hp=9f8aac6c518a554816a8a7731dc6125f79dc8bbc;hpb=6081884ff7c5a50b2a9f6615f7a864bdc5699bf2;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 9f8aac6..8e7c745 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -42,6 +42,7 @@ import java.io.FileWriter; import java.io.PrintWriter; import java.util.List; +import javax.swing.BoundedRangeModel; import javax.swing.SwingUtilities; import jalview.analysis.AnnotationSorter; @@ -256,8 +257,10 @@ public class AlignmentPanel extends GAlignmentPanel implements /** * 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. @@ -294,15 +297,30 @@ public class AlignmentPanel extends GAlignmentPanel implements 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, false, false); + 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 @@ -314,9 +332,41 @@ public class AlignmentPanel extends GAlignmentPanel implements 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( @@ -338,16 +388,17 @@ public class AlignmentPanel extends GAlignmentPanel implements // Also check annotation label widths if (includeAnnotations && al.getAlignmentAnnotation() != null) { - if (Jalview.isHeadlessMode()) + fm = c.getFontMetrics(getAlabels().getFont()); + + if (!legacy || Jalview.isHeadlessMode()) { - AnnotationLabels aal = this.getAlabels(); - int stringWidth = aal.drawLabels(null, false, idWidth, false, fm); + AnnotationLabels aal = getAlabels(); + int stringWidth = aal.drawLabels(null, false, idWidth, false, false, + fm, !visibleOnly); idWidth = Math.max(idWidth, stringWidth); } else { - fm = c.getFontMetrics(getAlabels().getFont()); - for (i = 0; i < al.getAlignmentAnnotation().length; i++) { AlignmentAnnotation aa = al.getAlignmentAnnotation()[i]; @@ -566,7 +617,8 @@ public class AlignmentPanel extends GAlignmentPanel implements // 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(); @@ -599,7 +651,7 @@ public class AlignmentPanel extends GAlignmentPanel implements Dimension e = idPanel.getSize(); int idWidth = e.width; boolean manuallyAdjusted = this.getIdPanel().getIdCanvas() - .manuallyAdjusted(); + .isManuallyAdjusted(); annotationScroller.setPreferredSize(new Dimension( manuallyAdjusted ? idWidth : annotationScroller.getWidth(), annotationHeight)); @@ -738,6 +790,22 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** + * Answers true if the panel has no horizontal scrollbar, or the scrollbar is + * at its rightmost position, else false. + * + * @return + */ + boolean isScrolledFullyRight() + { + if (hscroll == null) + { + return true; + } + BoundedRangeModel model = hscroll.getModel(); + return (model.getExtent() + model.getValue() >= model.getMaximum()); + } + + /** * Respond to adjustment event when horizontal or vertical scrollbar is * changed * @@ -898,6 +966,9 @@ public class AlignmentPanel extends GAlignmentPanel implements // need to make some adjustments idWidth -= (sc.getMinimumWrappedCanvasWidth() - sc.getWidth()); av.setIdWidth(idWidth); + av.getAlignPanel().getIdPanel().getIdCanvas() + .setManuallyAdjusted(true); + validateAnnotationDimensions(false); } } @@ -994,8 +1065,16 @@ public class AlignmentPanel extends GAlignmentPanel implements 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. @@ -1044,6 +1123,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } 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) */ @@ -1060,8 +1142,9 @@ public class AlignmentPanel extends GAlignmentPanel implements IdCanvas idCanvas = getIdPanel().getIdCanvas(); List 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); @@ -1085,7 +1168,7 @@ public class AlignmentPanel extends GAlignmentPanel implements int offset = getAlabels().getScrollOffset(); idGraphics.translate(0, -offset); idGraphics.translate(0, alignmentDrawnHeight); - getAlabels().drawComponent(idGraphics, idWidth); + getAlabels().drawComponentNotGUI(idGraphics, idWidth); idGraphics.translate(0, -alignmentDrawnHeight); /* @@ -1166,7 +1249,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * 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); @@ -1208,7 +1291,7 @@ public class AlignmentPanel extends GAlignmentPanel implements // 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"); @@ -1218,7 +1301,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } int w = getIdPanel().getWidth(); - w = this.calculateIdWidth(-1, true, true).width; + w = calculateIdWidth(-1, true, true).width; return (w > 0 ? w : calculateIdWidth().width); } @@ -1226,7 +1309,7 @@ public class AlignmentPanel extends GAlignmentPanel implements throws ImageOutputException { makeAlignmentImage(type, file, renderer, - BitmapImageSizing.nullBitmapImageSizing()); + BitmapImageSizing.defaultBitmapImageSizing()); } /** @@ -1846,5 +1929,4 @@ public class AlignmentPanel extends GAlignmentPanel implements overviewPanel = null; } } - }