X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=ee714833ff6ac0c4792f66efbb375637e0bf86d6;hb=8a2a0cda7067530f8481c2aec203e18d555f2dfd;hp=3dfb5105fcaf77d7c3312e8b0468d3bc5af44d09;hpb=b78a8a809f8ffbda3ca79e83d3df1c89064ef202;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 3dfb510..ee71483 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -50,6 +50,7 @@ import jalview.api.AlignmentViewPanel; 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; @@ -269,10 +270,7 @@ public class AlignmentPanel extends GAlignmentPanel implements 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 @@ -294,6 +292,14 @@ public class AlignmentPanel extends GAlignmentPanel implements 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. @@ -305,6 +311,12 @@ public class AlignmentPanel extends GAlignmentPanel implements */ 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( @@ -324,18 +336,29 @@ public class AlignmentPanel extends GAlignmentPanel implements } // 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); + } } } @@ -543,7 +566,7 @@ 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.outPrintln("NEEDS FIXING"); } validateAnnotationDimensions(true); addNotify(); @@ -567,21 +590,29 @@ public class AlignmentPanel extends GAlignmentPanel implements // 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(); } /** @@ -597,9 +628,10 @@ public class AlignmentPanel extends GAlignmentPanel implements 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) { @@ -633,7 +665,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - idSpaceFillerPanel1.setVisible(!wrap); + // idSpaceFillerPanel1.setVisible(!wrap); repaint(); } @@ -854,10 +886,27 @@ public class AlignmentPanel extends GAlignmentPanel implements 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 @@ -1172,10 +1221,12 @@ public class AlignmentPanel extends GAlignmentPanel implements } 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()); @@ -1196,6 +1247,7 @@ public class AlignmentPanel extends GAlignmentPanel implements final int borderBottomOffset = 5; AlignmentDimension aDimension = getAlignmentDimension(); + // todo use a lambda function in place of callback here? ImageWriterI writer = new ImageWriterI() { @@ -1266,7 +1318,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } - public void makePNGImageMap(File imgMapFile, String imageName) throws ImageOutputException + public void makePNGImageMap(File imgMapFile, String imageName) + throws ImageOutputException { // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS // //////////////////////////////////////////// @@ -1391,7 +1444,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } 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 @@ -1407,8 +1461,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { 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