From: Jim Procter Date: Wed, 23 Nov 2016 11:44:40 +0000 (+0000) Subject: Merge branch 'develop' of http://source.jalview.org/git/jalview into develop X-Git-Tag: Release_2_10_1~10^2~3 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=c605ffeba9f0df32f111c418763122a1b1ad42ec;hp=4d22ba3918844213aaf4c3f58da43f93146159d4;p=jalview.git Merge branch 'develop' of source.jalview.org/git/jalview into develop --- diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 235c81f..dc1f95b 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -960,7 +960,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } else { - return printUnwrapped(pwidth, pheight, pi, pg); + return printUnwrapped(pwidth, pheight, pi, pg, pg); } } @@ -981,110 +981,103 @@ public class AlignmentPanel extends GAlignmentPanel implements * @throws PrinterException * DOCUMENT ME! */ - public int printUnwrapped(int pwidth, int pheight, int pi, - Graphics... pg) + /** + * Draws the alignment image, including sequence ids, sequences, and + * annotation labels and annotations if shown, on either one or two Graphics + * context. + * + * @param pageWidth + * @param pageHeight + * @param pi + * @param idGraphics + * the graphics context for sequence ids and annotation labels + * @param alignmentGraphics + * the graphics context for sequences and annotations (may or may not + * be the same context as idGraphics) + * @return + * @throws PrinterException + */ + public int printUnwrapped(int pageWidth, int pageHeight, int pi, + Graphics idGraphics, Graphics alignmentGraphics) throws PrinterException { - boolean isMultiGraphics = pg.length > 1; - int G0 = 0; // Graphic index of idPanel graphics in multi-graphics mode or - // entire graphics for non mulit-graphics mode - int G1 = 0; // Graphic index of alignmentPanel graphics for multi-graphics - // mode - if (isMultiGraphics) - { - G0 = 0; - G1 = 1; - } - - int idWidth = getVisibleIdWidth(false); - FontMetrics fm = getFontMetrics(av.getFont()); - int scaleHeight = av.getCharHeight() + fm.getDescent(); - - pg[G0].setColor(Color.white); - pg[G0].fillRect(0, 0, pwidth, pheight); - pg[G0].setFont(av.getFont()); + final int idWidth = getVisibleIdWidth(false); - // ////////////////////////////////// - // / How many sequences and residues can we fit on a printable page? - int totalRes = (pwidth - idWidth) / av.getCharWidth(); + /* + * Get the horizontal offset to where we draw the sequences. + * This is idWidth if using a single Graphics context, else zero. + */ + final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 : idWidth; - int totalSeq = (pheight - scaleHeight) / av.getCharHeight() - 1; + FontMetrics fm = getFontMetrics(av.getFont()); + int charHeight = av.getCharHeight(); + int scaleHeight = charHeight + fm.getDescent(); - int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1; + idGraphics.setColor(Color.white); + idGraphics.fillRect(0, 0, pageWidth, pageHeight); + idGraphics.setFont(av.getFont()); - // /////////////////////////// - // / Only print these sequences and residues on this page - int startRes; + /* + * How many sequences and residues can we fit on a printable page? + */ + int totalRes = (pageWidth - idWidth) / av.getCharWidth(); - // /////////////////////////// - // / Only print these sequences and residues on this page - int endRes; + int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; - // /////////////////////////// - // / Only print these sequences and residues on this page - int startSeq; + int alignmentWidth = av.getAlignment().getWidth(); + int pagesWide = (alignmentWidth / totalRes) + 1; - // /////////////////////////// - // / Only print these sequences and residues on this page - int endSeq; - startRes = (pi % pagesWide) * totalRes; - endRes = (startRes + totalRes) - 1; + final int startRes = (pi % pagesWide) * totalRes; + int endRes = (startRes + totalRes) - 1; - if (endRes > (av.getAlignment().getWidth() - 1)) + if (endRes > (alignmentWidth - 1)) { - endRes = av.getAlignment().getWidth() - 1; + endRes = alignmentWidth - 1; } - startSeq = (pi / pagesWide) * totalSeq; - endSeq = startSeq + totalSeq; + final int startSeq = (pi / pagesWide) * totalSeq; + int endSeq = startSeq + totalSeq; - if (endSeq > av.getAlignment().getHeight()) + int alignmentHeight = av.getAlignment().getHeight(); + if (endSeq > alignmentHeight) { - endSeq = av.getAlignment().getHeight(); + endSeq = alignmentHeight; } - int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1) - * pheight; + int pagesHigh = ((alignmentHeight / totalSeq) + 1) + * pageHeight; if (av.isShowAnnotation()) { pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3; } - pagesHigh /= pheight; + pagesHigh /= pageHeight; if (pi >= (pagesWide * pagesHigh)) { return Printable.NO_SUCH_PAGE; } + final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + + 3; - // draw Scale - if (isMultiGraphics) - { - pg[G1].translate(0, 0); - getScalePanel().drawScale(pg[G1], startRes, endRes, - pwidth - idWidth, scaleHeight); - pg[G1].translate(-idWidth, scaleHeight); - } - else - { - pg[G0].translate(idWidth, 0); - getScalePanel().drawScale(pg[G0], startRes, endRes, pwidth - idWidth, - scaleHeight); - pg[G0].translate(-idWidth, scaleHeight); - } + /* + * draw the Scale at horizontal offset, then reset to top left (0, 0) + */ + alignmentGraphics.translate(alignmentGraphicsOffset, 0); + getScalePanel().drawScale(alignmentGraphics, startRes, endRes, + pageWidth - idWidth, scaleHeight); + alignmentGraphics.translate(-alignmentGraphicsOffset, 0); - // ////////////// - // Draw the ids + /* + * Draw the sequence ids, offset for scale height, + * then reset to top left (0, 0) + */ + idGraphics.translate(0, scaleHeight); + idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont()); Color currentColor = null; Color currentTextColor = null; - if (isMultiGraphics) - { - pg[G0].translate(0, scaleHeight); - } - pg[G0].setFont(getIdPanel().getIdCanvas().getIdfont()); - SequenceI seq; for (int i = startSeq; i < endSeq; i++) { @@ -1092,6 +1085,9 @@ public class AlignmentPanel extends GAlignmentPanel implements if ((av.getSelectionGroup() != null) && av.getSelectionGroup().getSequences(null).contains(seq)) { + /* + * gray out ids of sequences in selection group (if any) + */ currentColor = Color.gray; currentTextColor = Color.black; } @@ -1101,70 +1097,58 @@ public class AlignmentPanel extends GAlignmentPanel implements currentTextColor = Color.black; } - pg[G0].setColor(currentColor); - pg[G0].fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth, - av.getCharHeight()); + idGraphics.setColor(currentColor); + idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth, + charHeight); - pg[G0].setColor(currentTextColor); + idGraphics.setColor(currentTextColor); int xPos = 0; + String displayId = seq.getDisplayId(av.getShowJVSuffix()); if (av.isRightAlignIds()) { - fm = pg[G0].getFontMetrics(); + fm = idGraphics.getFontMetrics(); xPos = idWidth - - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix())) + - fm.stringWidth(displayId) - 4; } - pg[G0].drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos, - (((i - startSeq) * av.getCharHeight()) + av.getCharHeight()) - - (av.getCharHeight() / 5)); + idGraphics.drawString(displayId, xPos, + (((i - startSeq) * charHeight) + charHeight) + - (charHeight / 5)); } + idGraphics.setFont(av.getFont()); + idGraphics.translate(0, -scaleHeight); - pg[G0].setFont(av.getFont()); - + /* + * draw the sequences, offset for scale height, and id width (if using a + * single graphics context), then reset to (0, scale height) + */ + alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); + getSeqPanel().seqCanvas.drawPanel(alignmentGraphics, startRes, endRes, + startSeq, endSeq, 0); + alignmentGraphics.translate(-alignmentGraphicsOffset, 0); - // draw main sequence panel - pg[G0].translate(idWidth, 0); - if (isMultiGraphics) + if (av.isShowAnnotation() && (endSeq == alignmentHeight)) { - pg[G1].translate(idWidth, 0); - getSeqPanel().seqCanvas.drawPanel(pg[G1], startRes, endRes, - startSeq, endSeq, 0); - } - else - { - getSeqPanel().seqCanvas.drawPanel(pg[G0], startRes, endRes, startSeq, - endSeq, 0); - } + /* + * draw annotation labels; drawComponent() translates by + * getScrollOffset(), so compensate for that first; + * then reset to (0, scale height) + */ + int offset = getAlabels().getScrollOffset(); + idGraphics.translate(0, -offset); + idGraphics.translate(0, alignmentDrawnHeight); + getAlabels().drawComponent(idGraphics, idWidth); + idGraphics.translate(0, -alignmentDrawnHeight); - if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight())) - { - // draw annotation label - need to offset for current scroll position - int offset = -getAlabels().getScrollOffset(); - pg[G0].translate(0, offset); - pg[G0].translate(-idWidth - 3, - (endSeq - startSeq) * av.getCharHeight() + 3); - getAlabels().drawComponent(pg[G0], idWidth); - pg[G0].translate(idWidth + 3, 0); - pg[G0].translate(0, -offset); - if (isMultiGraphics) - { - // draw annotation - need to offset for current scroll position - // pg[G1].translate(0, offset); - pg[G1].translate(-idWidth - 3, - (endSeq - startSeq) * av.getCharHeight() + 3); - pg[G1].translate(idWidth + 3, 0); - getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), - av, pg[G1], -1, startRes, endRes + 1); - pg[G1].translate(0, -offset); - } - else - { - getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), - av, pg[G0], -1, startRes, endRes + 1); - pg[G0].translate(0, -offset); - } + /* + * draw the annotations starting at + * (idOffset, alignmentHeight) from (0, scaleHeight) + */ + alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight); + getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, + alignmentGraphics, -1, startRes, endRes + 1); } return Printable.PAGE_EXISTS; @@ -1363,22 +1347,23 @@ public class AlignmentPanel extends GAlignmentPanel implements aDimension.getWidth(), aDimension.getHeight() + boarderBottomOffset, file, imageTitle, alignFrame, pSessionId, headless); + Graphics graphics = im.getGraphics(); if (av.getWrapAlignment()) { - if (im.getGraphics() != null) + if (graphics != null) { printWrappedAlignment(aDimension.getWidth(), aDimension.getHeight() + boarderBottomOffset, 0, - im.getGraphics()); + graphics); im.writeImage(); } } else { - if (im.getGraphics() != null) + if (graphics != null) { printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), - 0, im.getGraphics()); + 0, graphics, graphics); im.writeImage(); } } diff --git a/src/jalview/io/HtmlSvgOutput.java b/src/jalview/io/HtmlSvgOutput.java index 2fabe9a..1ec3a4e 100644 --- a/src/jalview/io/HtmlSvgOutput.java +++ b/src/jalview/io/HtmlSvgOutput.java @@ -81,10 +81,12 @@ public class HtmlSvgOutput extends HTMLOutput "Hypertext Markup Language"); } - public int printUnwrapped(int pwidth, int pheight, int pi, Graphics... pg) + public int printUnwrapped(int pwidth, int pheight, int pi, + Graphics idGraphics, Graphics alignmentGraphics) throws PrinterException { - return ap.printUnwrapped(pwidth, pheight, pi, pg); + return ap.printUnwrapped(pwidth, pheight, pi, idGraphics, + alignmentGraphics); } public int printWrapped(int pwidth, int pheight, int pi, Graphics... pg)