X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;fp=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=ce87c01785119785c4123c42961e5653e8c4bd98;hp=2d057bb383e04e9379b25bc83185ff8bdd17ba29;hb=f680b9a507cc1643c9eead990e15026c1eca4e6e;hpb=265e81c0b3599a09c312f17188e3a892e9d96c4e diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 2d057bb..ce87c01 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -20,30 +20,6 @@ */ package jalview.gui; -import jalview.analysis.AnnotationSorter; -import jalview.api.AlignViewportI; -import jalview.api.AlignmentViewPanel; -import jalview.bin.Cache; -import jalview.bin.Console; -import jalview.bin.Jalview; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.HiddenColumns; -import jalview.datamodel.SearchResultsI; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceGroup; -import jalview.datamodel.SequenceI; -import jalview.gui.ImageExporter.ImageWriterI; -import jalview.io.HTMLOutput; -import jalview.jbgui.GAlignmentPanel; -import jalview.math.AlignmentDimension; -import jalview.schemes.ResidueProperties; -import jalview.structure.StructureSelectionManager; -import jalview.util.Comparison; -import jalview.util.ImageMaker; -import jalview.util.MessageManager; -import jalview.viewmodel.ViewportListenerI; -import jalview.viewmodel.ViewportRanges; - import java.awt.BorderLayout; import java.awt.Color; import java.awt.Container; @@ -68,6 +44,33 @@ import java.util.List; import javax.swing.SwingUtilities; +import jalview.analysis.AnnotationSorter; +import jalview.api.AlignViewportI; +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; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.gui.ImageExporter.ImageWriterI; +import jalview.io.HTMLOutput; +import jalview.io.exceptions.ImageOutputException; +import jalview.jbgui.GAlignmentPanel; +import jalview.math.AlignmentDimension; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureSelectionManager; +import jalview.util.Comparison; +import jalview.util.ImageMaker; +import jalview.util.MessageManager; +import jalview.util.imagemaker.BitmapImageSizing; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; + /** * DOCUMENT ME! * @@ -229,8 +232,9 @@ public class AlignmentPanel extends GAlignmentPanel implements // set idCanvas bufferedImage to null // to prevent drawing old image FontMetrics fm = getFontMetrics(av.getFont()); - - // update the flag controlling whether the grid is too small to render the font + + // update the flag controlling whether the grid is too small to render the + // font av.validCharWidth = fm.charWidth('M') <= av.getCharWidth(); scalePanelHolder.setPreferredSize( @@ -266,10 +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 @@ -291,6 +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. @@ -302,6 +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( @@ -321,18 +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 = getAlabels(); + int stringWidth = aal.drawLabels(null, false, idWidth, false, 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); + } } } @@ -540,7 +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(); @@ -564,21 +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(); } /** @@ -594,9 +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) { @@ -630,7 +665,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - idSpaceFillerPanel1.setVisible(!wrap); + // idSpaceFillerPanel1.setVisible(!wrap); repaint(); } @@ -851,10 +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 @@ -1012,7 +1064,7 @@ public class AlignmentPanel extends GAlignmentPanel implements List selection = av.getSelectionGroup() == null ? null : av.getSelectionGroup().getSequences(null); idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1, - selection); + selection, false); idGraphics.setFont(av.getFont()); idGraphics.translate(0, -scaleHeight); @@ -1036,7 +1088,7 @@ 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); /* @@ -1045,6 +1097,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight); + updateLayout(); getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, alignmentGraphics, -1, startRes, endRes + 1); } @@ -1116,7 +1169,7 @@ 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); @@ -1168,21 +1221,33 @@ 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 + { + makeAlignmentImage(type, file, renderer, + BitmapImageSizing.nullBitmapImageSizing()); + } + /** * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and * writes it to the specified file * * @param type * @param file + * @param textrenderer + * @param bitmapscale */ - void makeAlignmentImage(ImageMaker.TYPE type, File file) + void makeAlignmentImage(ImageMaker.TYPE type, File file, String renderer, + BitmapImageSizing userBis) throws ImageOutputException { final int borderBottomOffset = 5; AlignmentDimension aDimension = getAlignmentDimension(); + // todo use a lambda function in place of callback here? ImageWriterI writer = new ImageWriterI() { @@ -1208,7 +1273,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int imageWidth = aDimension.getWidth(); int imageHeight = aDimension.getHeight() + borderBottomOffset; String of = MessageManager.getString("label.alignment"); - exporter.doExport(file, this, imageWidth, imageHeight, of); + exporter.doExport(file, this, imageWidth, imageHeight, of, renderer, + userBis); } /** @@ -1253,6 +1319,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } public void makePNGImageMap(File imgMapFile, String imageName) + throws ImageOutputException { // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS // //////////////////////////////////////////// @@ -1377,7 +1444,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } catch (Exception ex) { - ex.printStackTrace(); + throw new ImageOutputException( + "couldn't write ImageMap due to unexpected error", ex); } } // /////////END OF IMAGE MAP @@ -1393,8 +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