X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=dc1f95ba377622a28e0e13b82d237e4a49a7e312;hb=6168111321deafec25337c6c59210f14f857041d;hp=b16e2436bc6938bd5abab4d6773f1e9a11ee5838;hpb=b07c7cb77f73eecaea77b66b9b5f7f9071e0e1e0;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index b16e243..dc1f95b 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -25,7 +25,7 @@ import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; import jalview.datamodel.AlignmentI; -import jalview.datamodel.SearchResults; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; @@ -101,6 +101,8 @@ public class AlignmentPanel extends GAlignmentPanel implements */ private boolean dontScrollComplement; + private PropertyChangeListener propertyChangeListener; + /** * Creates a new AlignmentPanel object. * @@ -135,7 +137,7 @@ public class AlignmentPanel extends GAlignmentPanel implements vscroll.addAdjustmentListener(this); final AlignmentPanel ap = this; - av.addPropertyChangeListener(new PropertyChangeListener() + propertyChangeListener = new PropertyChangeListener() { @Override public void propertyChange(PropertyChangeEvent evt) @@ -146,7 +148,8 @@ public class AlignmentPanel extends GAlignmentPanel implements alignmentChanged(); } } - }); + }; + av.addPropertyChangeListener(propertyChangeListener); fontChanged(); adjustAnnotationHeight(); updateLayout(); @@ -294,7 +297,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * Highlight the given results on the alignment. * */ - public void highlightSearchResults(SearchResults results) + public void highlightSearchResults(SearchResultsI results) { scrollToPosition(results); getSeqPanel().seqCanvas.highlightSearchResults(results); @@ -306,7 +309,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * * @param results */ - public boolean scrollToPosition(SearchResults results) + public boolean scrollToPosition(SearchResultsI results) { return scrollToPosition(results, 0, true, false); } @@ -319,7 +322,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param redrawOverview * @return */ - public boolean scrollToPosition(SearchResults searchResults, + public boolean scrollToPosition(SearchResultsI searchResults, boolean redrawOverview) { return scrollToPosition(searchResults, 0, redrawOverview, false); @@ -339,7 +342,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * if true, try to centre the search results horizontally in the view * @return false if results were not found */ - public boolean scrollToPosition(SearchResults results, + public boolean scrollToPosition(SearchResultsI results, int verticalOffset, boolean redrawOverview, boolean centre) { int startv, endv, starts, ends; @@ -953,11 +956,11 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.getWrapAlignment()) { - return printWrappedAlignment(pg, pwidth, pheight, pi); + return printWrappedAlignment(pwidth, pheight, pi, pg); } else { - return printUnwrapped(pg, pwidth, pheight, pi); + return printUnwrapped(pwidth, pheight, pi, pg, pg); } } @@ -978,84 +981,103 @@ public class AlignmentPanel extends GAlignmentPanel implements * @throws PrinterException * DOCUMENT ME! */ - public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) + /** + * 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 { - int idWidth = getVisibleIdWidth(false); - FontMetrics fm = getFontMetrics(av.getFont()); - int scaleHeight = av.getCharHeight() + fm.getDescent(); + final int idWidth = getVisibleIdWidth(false); - pg.setColor(Color.white); - pg.fillRect(0, 0, pwidth, pheight); - pg.setFont(av.getFont()); - - // ////////////////////////////////// - // / 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 - pg.translate(idWidth, 0); - getScalePanel().drawScale(pg, startRes, endRes, pwidth - idWidth, - scaleHeight); - pg.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; - pg.setFont(getIdPanel().getIdCanvas().getIdfont()); - SequenceI seq; for (int i = startSeq; i < endSeq; i++) { @@ -1063,6 +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; } @@ -1072,45 +1097,58 @@ public class AlignmentPanel extends GAlignmentPanel implements currentTextColor = Color.black; } - pg.setColor(currentColor); - pg.fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth, - av.getCharHeight()); + idGraphics.setColor(currentColor); + idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth, + charHeight); - pg.setColor(currentTextColor); + idGraphics.setColor(currentTextColor); int xPos = 0; + String displayId = seq.getDisplayId(av.getShowJVSuffix()); if (av.isRightAlignIds()) { - fm = pg.getFontMetrics(); + fm = idGraphics.getFontMetrics(); xPos = idWidth - - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix())) + - fm.stringWidth(displayId) - 4; } - pg.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.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.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, - endSeq, 0); - - if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight())) - { - // draw annotation - need to offset for current scroll position - int offset = -getAlabels().getScrollOffset(); - pg.translate(0, offset); - pg.translate(-idWidth - 3, (endSeq - startSeq) * av.getCharHeight() - + 3); - getAlabels().drawComponent(pg, idWidth); - pg.translate(idWidth + 3, 0); + if (av.isShowAnnotation() && (endSeq == alignmentHeight)) + { + /* + * 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); + + /* + * draw the annotations starting at + * (idOffset, alignmentHeight) from (0, scaleHeight) + */ + alignmentGraphics.translate(alignmentGraphicsOffset, alignmentDrawnHeight); getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, - pg, -1, startRes, endRes + 1); - pg.translate(0, -offset); + alignmentGraphics, -1, startRes, endRes + 1); } return Printable.PAGE_EXISTS; @@ -1133,8 +1171,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * @throws PrinterException * DOCUMENT ME! */ - public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, - int pi) throws PrinterException + public int printWrappedAlignment(int pwidth, int pheight, int pi, + Graphics pg) throws PrinterException { int annotationHeight = 0; AnnotationLabels labels = null; @@ -1269,7 +1307,7 @@ public class AlignmentPanel extends GAlignmentPanel implements void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file) { - int boarderBottomOffset = 0; + int boarderBottomOffset = 5; long pSessionId = System.currentTimeMillis(); headless = (System.getProperty("java.awt.headless") != null && System .getProperty("java.awt.headless").equals("true")); @@ -1278,7 +1316,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (file != null) { alignFrame.setProgressBar(MessageManager.formatMessage( - "status.saving_file", new Object[] { type.getLabel() }), + "status.saving_file", new Object[] { type.getLabel() }), pSessionId); } } @@ -1307,23 +1345,25 @@ public class AlignmentPanel extends GAlignmentPanel implements im = new jalview.util.ImageMaker(this, type, imageAction, aDimension.getWidth(), aDimension.getHeight() - + boarderBottomOffset, file, - imageTitle, alignFrame, pSessionId, headless); + + boarderBottomOffset, file, imageTitle, + alignFrame, pSessionId, headless); + Graphics graphics = im.getGraphics(); if (av.getWrapAlignment()) { - if (im.getGraphics() != null) + if (graphics != null) { - printWrappedAlignment(im.getGraphics(), aDimension.getWidth(), - aDimension.getHeight() + boarderBottomOffset, 0); + printWrappedAlignment(aDimension.getWidth(), + aDimension.getHeight() + boarderBottomOffset, 0, + graphics); im.writeImage(); } } else { - if (im.getGraphics() != null) + if (graphics != null) { - printUnwrapped(im.getGraphics(), aDimension.getWidth(), - aDimension.getHeight(), 0); + printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), + 0, graphics, graphics); im.writeImage(); } } @@ -1595,8 +1635,18 @@ public class AlignmentPanel extends GAlignmentPanel implements PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas); PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas()); PaintRefresher.RemoveComponent(this); + + /* + * try to ensure references are nulled + */ + if (annotationPanel != null) + { + annotationPanel.dispose(); + } + if (av != null) { + av.removePropertyChangeListener(propertyChangeListener); jalview.structure.StructureSelectionManager ssm = av .getStructureSelectionManager(); ssm.removeStructureViewerListener(getSeqPanel(), null); @@ -1604,7 +1654,7 @@ public class AlignmentPanel extends GAlignmentPanel implements ssm.removeCommandListener(av); ssm.removeStructureViewerListener(getSeqPanel(), null); ssm.removeSelectionListener(getSeqPanel()); - av.setAlignment(null); + av.dispose(); av = null; } else @@ -1775,14 +1825,14 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param verticalOffset * the number of visible sequences to show above the mapped region */ - public void scrollToCentre(SearchResults sr, int verticalOffset) + public void scrollToCentre(SearchResultsI sr, int verticalOffset) { /* * To avoid jumpy vertical scrolling (if some sequences are gapped or not * mapped), we can make the scroll-to location a sequence above the one * actually mapped. */ - SequenceI mappedTo = sr.getResultSequence(0); + SequenceI mappedTo = sr.getResults().get(0).getSequence(); List seqs = av.getAlignment().getSequences(); /*