X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=f06ca94a1acf8557c3797fb95ffee7969011be70;hb=608002f963630dd631941e34f1a6a93b6dcbd823;hp=e29a0e2df84f47afb4b3e79f09f2d4caec54884f;hpb=e81459b192f4d635c1cd96befa7b14992d12ee5e;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index e29a0e2..f06ca94 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -76,6 +76,7 @@ public class AlignmentPanel extends GAlignmentPanel implements private IdPanel idPanel; private boolean headless; + IdwidthAdjuster idwidthAdjuster; /** DOCUMENT ME!! */ @@ -98,7 +99,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * Flag set while scrolling to follow complementary cDNA/protein scroll. When * true, suppresses invoking the same method recursively. */ - private boolean followingComplementScroll; + private boolean dontScrollComplement; /** * Creates a new AlignmentPanel object. @@ -136,6 +137,7 @@ public class AlignmentPanel extends GAlignmentPanel implements final AlignmentPanel ap = this; av.addPropertyChangeListener(new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) @@ -155,6 +157,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { return av; } + public void alignmentChanged() { av.alignmentChanged(this); @@ -177,8 +180,7 @@ public class AlignmentPanel extends GAlignmentPanel implements scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight() + fm.getDescent())); idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av - .getCharHeight() - + fm.getDescent())); + .getCharHeight() + fm.getDescent())); getIdPanel().getIdCanvas().gg = null; getSeqPanel().seqCanvas.img = null; @@ -317,7 +319,8 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param redrawOverview * @return */ - public boolean scrollToPosition(SearchResults searchResults, boolean redrawOverview) + public boolean scrollToPosition(SearchResults searchResults, + boolean redrawOverview) { return scrollToPosition(searchResults, 0, redrawOverview, false); } @@ -337,8 +340,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @return false if results were not found */ public boolean scrollToPosition(SearchResults results, - int verticalOffset, - boolean redrawOverview, boolean centre) + int verticalOffset, boolean redrawOverview, boolean centre) { int startv, endv, starts, ends; // TODO: properly locate search results in view when large numbers of hidden @@ -363,8 +365,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int start = r[0]; int end = r[1]; // DEBUG -// System.err.println(this.av.viewName + " Seq : " + seqIndex -// + " Scroll to " + start + "," + end); + // System.err.println(this.av.viewName + " Seq : " + seqIndex + // + " Scroll to " + start + "," + end); /* * To centre results, scroll to positions half the visible width @@ -508,6 +510,7 @@ 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 @@ -565,6 +568,9 @@ public class AlignmentPanel extends GAlignmentPanel implements annotationScroller.setPreferredSize(new Dimension(annotationScroller .getWidth(), annotationHeight)); + Dimension e = idPanel.getSize(); + alabels.setSize(new Dimension(e.width, annotationHeight)); + annotationSpaceFillerHolder.setPreferredSize(new Dimension( annotationSpaceFillerHolder.getWidth(), annotationHeight)); annotationScroller.validate(); @@ -728,7 +734,14 @@ public class AlignmentPanel extends GAlignmentPanel implements x = 0; } + /* + * each scroll adjustment triggers adjustmentValueChanged, which resets the + * 'do not scroll complement' flag; ensure it is the same for both + * operations + */ + boolean flag = isDontScrollComplement(); hscroll.setValues(x, hextent, 0, width); + setDontScrollComplement(flag); vscroll.setValues(y, vextent, 0, height); } @@ -738,6 +751,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param evt * DOCUMENT ME! */ + @Override public void adjustmentValueChanged(AdjustmentEvent evt) { int oldX = av.getStartRes(); @@ -747,7 +761,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { int x = hscroll.getValue(); av.setStartRes(x); - av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1); + av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av + .getCharWidth())) - 1); } if (evt.getSource() == vscroll) @@ -770,6 +785,7 @@ public class AlignmentPanel extends GAlignmentPanel implements // as preference setting SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { setScrollValues(av.getStartRes(), av.getStartSeq()); @@ -826,9 +842,9 @@ public class AlignmentPanel extends GAlignmentPanel implements * If there is one, scroll the (Protein/cDNA) complementary alignment to * match, unless we are ourselves doing that. */ - if (isFollowingComplementScroll()) + if (isDontScrollComplement()) { - setFollowingComplementScroll(false); + setDontScrollComplement(false); } else { @@ -840,17 +856,18 @@ 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(), av.isShowAutocalculatedAbove()); - sorter.sort(getAlignment() - .getAlignmentAnnotation(), + sorter.sort(getAlignment().getAlignmentAnnotation(), av.getSortAnnotationsBy()); repaint(); if (updateOverview) { + // TODO: determine if this paintAlignment changed structure colours av.getStructureSelectionManager().sequenceColoursChanged(this); if (overviewPanel != null) @@ -866,6 +883,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param g * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { invalidate(); @@ -875,6 +893,12 @@ public class AlignmentPanel extends GAlignmentPanel implements hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12)); validate(); + /* + * set scroll bar positions; first suppress this being 'followed' in any + * complementary split pane + */ + setDontScrollComplement(true); + if (av.getWrapAlignment()) { int maxwidth = av.getAlignment().getWidth(); @@ -918,6 +942,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @throws PrinterException * DOCUMENT ME! */ + @Override public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { @@ -1062,9 +1087,7 @@ public class AlignmentPanel extends GAlignmentPanel implements - 4; } - pg.drawString( - seq.getDisplayId(av.getShowJVSuffix()), - xPos, + pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos, (((i - startSeq) * av.getCharHeight()) + av.getCharHeight()) - (av.getCharHeight() / 5)); } @@ -1073,7 +1096,8 @@ public class AlignmentPanel extends GAlignmentPanel implements // draw main sequence panel pg.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0); + getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, + endSeq, 0); if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight())) { @@ -1175,12 +1199,14 @@ public class AlignmentPanel extends GAlignmentPanel implements } if (labels != null) { - pg.translate(-3, ypos - + (av.getAlignment().getHeight() * av.getCharHeight())); + pg.translate(-3, + ypos + (av.getAlignment().getHeight() * av.getCharHeight())); pg.setFont(av.getFont()); labels.drawComponent(pg, idWidth); - pg.translate(+3, -ypos + pg.translate( + +3, + -ypos - (av.getAlignment().getHeight() * av .getCharHeight())); } @@ -1190,8 +1216,8 @@ public class AlignmentPanel extends GAlignmentPanel implements pg.translate(idWidth, 0); - getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, - 0); + getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, + totalHeight, 0); if ((pi * pheight) < totalHeight) { @@ -1243,14 +1269,17 @@ public class AlignmentPanel extends GAlignmentPanel implements void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file) { - long progress = System.currentTimeMillis(); + 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 { @@ -1277,7 +1306,7 @@ public class AlignmentPanel extends GAlignmentPanel implements im = new jalview.util.ImageMaker(this, type, imageAction, aDimension.getWidth(), aDimension.getHeight(), file, - imageTitle); + imageTitle, alignFrame, pSessionId, headless); if (av.getWrapAlignment()) { if (im.getGraphics() != null) @@ -1296,6 +1325,7 @@ public class AlignmentPanel extends GAlignmentPanel implements im.writeImage(); } } + } catch (OutOfMemoryError err) { // Be noisy here. @@ -1309,10 +1339,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } } finally { - if (alignFrame != null && !headless) - { - alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress); - } + } } @@ -1376,6 +1403,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile); } + public void makePNGImageMap(File imgMapFile, String imageName) { // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS @@ -1413,8 +1441,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.getAlignment().isNucleotide()) { triplet = ResidueProperties.nucleotideName.get(seq - .getCharAt(res) - + ""); + .getCharAt(res) + ""); } else { @@ -1436,8 +1463,7 @@ public class AlignmentPanel extends GAlignmentPanel implements text.append("