X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=235c81f068ed8eb17a226e1c780e95bc86b0383e;hb=134576f5b34894218bdc4c5ce5e27fa18ad973bd;hp=3031cd5e6dfd9f330fb132c29d58962a87553807;hpb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 3031cd5..235c81f 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -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. * @@ -135,8 +137,9 @@ 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) { if (evt.getPropertyName().equals("alignment")) @@ -145,7 +148,8 @@ public class AlignmentPanel extends GAlignmentPanel implements alignmentChanged(); } } - }); + }; + av.addPropertyChangeListener(propertyChangeListener); fontChanged(); adjustAnnotationHeight(); updateLayout(); @@ -293,7 +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); @@ -305,7 +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); } @@ -318,7 +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); @@ -338,7 +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; @@ -509,6 +513,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * automatically adjust annotation panel height for new annotation whilst * ensuring the alignment is still visible. */ + @Override public void adjustAnnotationHeight() { // TODO: display vertical annotation scrollbar if necessary @@ -749,6 +754,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param evt * DOCUMENT ME! */ + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { int oldX = av.getStartRes(); @@ -782,6 +788,7 @@ public class AlignmentPanel extends GAlignmentPanel implements // as preference setting SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { setScrollValues(av.getStartRes(), av.getStartSeq()); @@ -852,6 +859,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * Repaint the alignment including the annotations and overview panels (if * shown). */ + @Override public void paintAlignment(boolean updateOverview) { final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), @@ -878,6 +886,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param g * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { invalidate(); @@ -936,6 +945,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @throws PrinterException * DOCUMENT ME! */ + @Override public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { @@ -946,11 +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); } } @@ -971,16 +981,28 @@ public class AlignmentPanel extends GAlignmentPanel implements * @throws PrinterException * DOCUMENT ME! */ - public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) + public int printUnwrapped(int pwidth, int pheight, int pi, + Graphics... pg) 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.setColor(Color.white); - pg.fillRect(0, 0, pwidth, pheight); - pg.setFont(av.getFont()); + pg[G0].setColor(Color.white); + pg[G0].fillRect(0, 0, pwidth, pheight); + pg[G0].setFont(av.getFont()); // ////////////////////////////////// // / How many sequences and residues can we fit on a printable page? @@ -1037,17 +1059,31 @@ public class AlignmentPanel extends GAlignmentPanel implements } // draw Scale - pg.translate(idWidth, 0); - getScalePanel().drawScale(pg, startRes, endRes, pwidth - idWidth, - scaleHeight); - pg.translate(-idWidth, scaleHeight); + 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 ids Color currentColor = null; Color currentTextColor = null; - pg.setFont(getIdPanel().getIdCanvas().getIdfont()); + if (isMultiGraphics) + { + pg[G0].translate(0, scaleHeight); + } + pg[G0].setFont(getIdPanel().getIdCanvas().getIdfont()); SequenceI seq; for (int i = startSeq; i < endSeq; i++) @@ -1065,45 +1101,70 @@ public class AlignmentPanel extends GAlignmentPanel implements currentTextColor = Color.black; } - pg.setColor(currentColor); - pg.fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth, + pg[G0].setColor(currentColor); + pg[G0].fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth, av.getCharHeight()); - pg.setColor(currentTextColor); + pg[G0].setColor(currentTextColor); int xPos = 0; if (av.isRightAlignIds()) { - fm = pg.getFontMetrics(); + fm = pg[G0].getFontMetrics(); xPos = idWidth - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix())) - 4; } - pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos, + pg[G0].drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos, (((i - startSeq) * av.getCharHeight()) + av.getCharHeight()) - (av.getCharHeight() / 5)); } - pg.setFont(av.getFont()); + pg[G0].setFont(av.getFont()); + // draw main sequence panel - pg.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, - endSeq, 0); + pg[G0].translate(idWidth, 0); + if (isMultiGraphics) + { + 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); + } if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight())) { - // draw annotation - need to offset for current scroll position + // draw annotation label - 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); - getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, - pg, -1, startRes, endRes + 1); - pg.translate(0, -offset); + 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); + } } return Printable.PAGE_EXISTS; @@ -1126,8 +1187,8 @@ 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; @@ -1262,14 +1323,18 @@ public class AlignmentPanel extends GAlignmentPanel implements void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file) { - long progress = System.currentTimeMillis(); + int boarderBottomOffset = 5; + long pSessionId = System.currentTimeMillis(); headless = (System.getProperty("java.awt.headless") != null && System .getProperty("java.awt.headless").equals("true")); if (alignFrame != null && !headless) { - alignFrame.setProgressBar(MessageManager.formatMessage( - "status.saving_file", new Object[] { type.getLabel() }), - progress); + if (file != null) + { + alignFrame.setProgressBar(MessageManager.formatMessage( + "status.saving_file", new Object[] { type.getLabel() }), + pSessionId); + } } try { @@ -1295,14 +1360,16 @@ public class AlignmentPanel extends GAlignmentPanel implements } im = new jalview.util.ImageMaker(this, type, imageAction, - aDimension.getWidth(), aDimension.getHeight(), file, - imageTitle); + aDimension.getWidth(), aDimension.getHeight() + + boarderBottomOffset, file, imageTitle, + alignFrame, pSessionId, headless); if (av.getWrapAlignment()) { if (im.getGraphics() != null) { - printWrappedAlignment(im.getGraphics(), aDimension.getWidth(), - aDimension.getHeight(), 0); + printWrappedAlignment(aDimension.getWidth(), + aDimension.getHeight() + boarderBottomOffset, 0, + im.getGraphics()); im.writeImage(); } } @@ -1310,11 +1377,12 @@ public class AlignmentPanel extends GAlignmentPanel implements { if (im.getGraphics() != null) { - printUnwrapped(im.getGraphics(), aDimension.getWidth(), - aDimension.getHeight(), 0); + printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), + 0, im.getGraphics()); im.writeImage(); } } + } catch (OutOfMemoryError err) { // Be noisy here. @@ -1328,12 +1396,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } } finally { - if (alignFrame != null && !headless) - { - alignFrame.setProgressBar( - MessageManager.getString("status.export_complete"), - progress); - } + } } @@ -1587,8 +1650,18 @@ 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); @@ -1596,7 +1669,7 @@ public class AlignmentPanel extends GAlignmentPanel implements ssm.removeCommandListener(av); ssm.removeStructureViewerListener(getSeqPanel(), null); ssm.removeSelectionListener(getSeqPanel()); - av.setAlignment(null); + av.dispose(); av = null; } else @@ -1767,14 +1840,14 @@ 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(); /*