X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=b4647ae36692bd2e997be98493ab974699471dfe;hb=b91c00e8dba2b753769ea921dbe4404f49896db0;hp=bbd9f72b8550e3a3855d46136ff8ea18f14b1aba;hpb=106634777c0910504d9c1617d6307b70581fd3c8;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java old mode 100755 new mode 100644 index bbd9f72..b4647ae --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,20 +1,19 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . */ package jalview.gui; @@ -26,19 +25,21 @@ import java.awt.event.*; import java.awt.print.*; import javax.swing.*; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; import jalview.datamodel.*; import jalview.jbgui.*; import jalview.schemes.*; -import jalview.structure.SelectionSource; +import jalview.structure.StructureSelectionManager; /** * DOCUMENT ME! * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.161 $ */ public class AlignmentPanel extends GAlignmentPanel implements - AdjustmentListener, Printable + AdjustmentListener, Printable, AlignmentViewPanel { public AlignViewport av; @@ -70,9 +71,9 @@ public class AlignmentPanel extends GAlignmentPanel implements * Creates a new AlignmentPanel object. * * @param af - * DOCUMENT ME! + * DOCUMENT ME! * @param av - * DOCUMENT ME! + * DOCUMENT ME! */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { @@ -170,15 +171,31 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public Dimension calculateIdWidth() { + // calculate sensible default width when no preference is available + + int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); + int maxwidth = Math.max(20, + Math.min(afwidth - 200, (int) 2 * afwidth / 3)); + return calculateIdWidth(maxwidth); + } + + /** + * Calculate the width of the alignment labels based on the displayed names + * and any bounds on label width set in preferences. + * + * @param maxwidth + * -1 or maximum width allowed for IdWidth + * @return Dimension giving the maximum width of the alignment label panel + * that should be used. + */ + public Dimension calculateIdWidth(int maxwidth) + { Container c = new Container(); FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(), Font.ITALIC, av.font.getSize())); AlignmentI al = av.getAlignment(); - int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); - int maxwidth = Math.max(20, Math.min(afwidth - 200, (int) 2 * afwidth - / 3)); int i = 0; int idWidth = 0; String id; @@ -217,83 +234,117 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - return new Dimension(Math.min(maxwidth, idWidth), 12); + return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth, + idWidth), 12); } /** - * DOCUMENT ME! + * Highlight the given results on the alignment. * - * @param results - * DOCUMENT ME! */ public void highlightSearchResults(SearchResults results) { scrollToPosition(results); seqPanel.seqCanvas.highlightSearchResults(results); } + /** - * scroll the view to show the position of the highlighted - * region in results (if any) and redraw the overview + * scroll the view to show the position of the highlighted region in results + * (if any) and redraw the overview + * * @param results */ - public boolean scrollToPosition(SearchResults results) { + public boolean scrollToPosition(SearchResults results) + { return scrollToPosition(results, true); } + /** - * scroll the view to show the position of the highlighted - * region in results (if any) + * scroll the view to show the position of the highlighted region in results + * (if any) + * * @param results - * @param redrawOverview - when set, the overview will be recalculated (takes longer) + * @param redrawOverview + * - when set, the overview will be recalculated (takes longer) * @return false if results were not found */ - public boolean scrollToPosition(SearchResults results, boolean redrawOverview) { - // TODO: properly locate search results in view when large numbers of hidden columns exist before highlighted region + public boolean scrollToPosition(SearchResults results, + boolean redrawOverview) + { + int startv, endv, starts, ends, width; + // TODO: properly locate search results in view when large numbers of hidden + // columns exist before highlighted region // do we need to scroll the panel? - if (results != null && results.getSize()>0) + // TODO: tons of nullpointereexceptions raised here. + if (results != null && results.getSize() > 0 && av != null + && av.getAlignment() != null) { - int seqIndex = av.alignment.findIndex(results); - if (seqIndex==-1) + int seqIndex = av.getAlignment().findIndex(results); + if (seqIndex == -1) { return false; } - SequenceI seq = av.alignment.getSequenceAt(seqIndex); - - int [] r = results.getResults(seq, seq.getStart(), seq.getEnd()); - if (r==null) + SequenceI seq = av.getAlignment().getSequenceAt(seqIndex); + + int[] r = results.getResults(seq, 0, av.getAlignment().getWidth()); + if (r == null) { return false; } int start = r[0]; int end = r[1]; - if (start<0) + // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); // + // DEBUG + if (start < 0) { return false; } - if (end==seq.getEnd()) + if (end == seq.getEnd()) { return false; } + if (av.hasHiddenColumns()) + { + start = av.getColumnSelection().findColumnPosition(start); + end = av.getColumnSelection().findColumnPosition(end); + if (start == end) + { + if (!av.getColumnSelection().isVisible(r[0])) + { + // don't scroll - position isn't visible + return false; + } + } + } if (!av.wrapAlignment) { - if ((av.getStartRes() >= start) - || (av.getEndRes() <= end)) + if ((startv = av.getStartRes()) >= start) { - setScrollValues(start-1, seqIndex); - } else if ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex)) + setScrollValues(start - 1, seqIndex); + } + else if ((endv = av.getEndRes()) <= end) + { + setScrollValues(startv + 1 + end - endv, seqIndex); + } + else if ((starts = av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(), seqIndex); } + else if ((ends = av.getEndSeq()) <= seqIndex) + { + setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); + } } else { scrollToWrappedVisible(start); } } - if (!redrawOverview && overviewPanel!=null) + if (redrawOverview && overviewPanel != null) { overviewPanel.setBoxPosition(); - } - paintAlignment(!redrawOverview); + } + paintAlignment(redrawOverview); return true; } @@ -301,7 +352,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { int cwidth = seqPanel.seqCanvas .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); - if (res < av.getStartRes() || res >= (av.getStartRes()+cwidth)) + if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth)) { vscroll.setValue((res / cwidth)); av.startRes = vscroll.getValue() * cwidth; @@ -323,7 +374,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param op - * DOCUMENT ME! + * DOCUMENT ME! */ public void setOverviewPanel(OverviewPanel op) { @@ -331,10 +382,10 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * Hide or show annotation panel + * */ public void setAnnotationVisible(boolean b) { @@ -346,6 +397,10 @@ public class AlignmentPanel extends GAlignmentPanel implements repaint(); } + /** + * automatically adjust annotation panel height for new annotation whilst + * ensuring the alignment is still visible. + */ public void adjustAnnotationHeight() { // TODO: display vertical annotation scrollbar if necessary @@ -354,7 +409,17 @@ public class AlignmentPanel extends GAlignmentPanel implements { System.out.println("NEEDS FIXING"); } + validateAnnotationDimensions(true); + addNotify(); + paintAlignment(true); + } + /** + * calculate the annotation dimensions and refresh slider values accordingly. + * need to do repaints/notifys afterwards. + */ + protected void validateAnnotationDimensions(boolean adjustPanelHeight) + { int height = annotationPanel.adjustPanelHeight(); if (hscroll.isVisible()) @@ -365,7 +430,11 @@ public class AlignmentPanel extends GAlignmentPanel implements { height = alignFrame.getHeight() / 2; } - + if (!adjustPanelHeight) + { + // maintain same window layout whilst updating sliders + height = annotationScroller.getSize().height; + } hscroll.addNotify(); annotationScroller.setPreferredSize(new Dimension(annotationScroller @@ -374,14 +443,14 @@ public class AlignmentPanel extends GAlignmentPanel implements annotationSpaceFillerHolder.setPreferredSize(new Dimension( annotationSpaceFillerHolder.getWidth(), height)); annotationScroller.validate();// repaint(); - repaint(); + annotationScroller.addNotify(); } /** * DOCUMENT ME! * * @param wrap - * DOCUMENT ME! + * DOCUMENT ME! */ public void setWrapAlignment(boolean wrap) { @@ -416,7 +485,7 @@ public class AlignmentPanel extends GAlignmentPanel implements return false; } - fastPaint = false; + //fastPaint = false; vscroll.setValue(vscroll.getValue() - 1); } else @@ -426,11 +495,11 @@ public class AlignmentPanel extends GAlignmentPanel implements return false; } - fastPaint = false; + //fastPaint = false; vscroll.setValue(vscroll.getValue() + 1); } - fastPaint = true; + //fastPaint = true; return true; } @@ -439,7 +508,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param right - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! */ @@ -452,7 +521,7 @@ public class AlignmentPanel extends GAlignmentPanel implements return false; } - fastPaint = false; + //fastPaint = false; hscroll.setValue(hscroll.getValue() - 1); } else @@ -462,33 +531,35 @@ public class AlignmentPanel extends GAlignmentPanel implements return false; } - fastPaint = false; + //fastPaint = false; hscroll.setValue(hscroll.getValue() + 1); } - fastPaint = true; + //fastPaint = true; return true; } /** - * DOCUMENT ME! + * Adjust row/column scrollers to show a visible position in the alignment. * * @param x - * DOCUMENT ME! + * visible column to scroll to DOCUMENT ME! * @param y - * DOCUMENT ME! + * visible row to scroll to + * */ public void setScrollValues(int x, int y) { - if (av==null || av.alignment==null) + // System.err.println("Scroll to "+x+","+y); + if (av == null || av.getAlignment() == null) { return; } - int width = av.alignment.getWidth(); - int height = av.alignment.getHeight(); + int width = av.getAlignment().getWidth(); + int height = av.getAlignment().getHeight(); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { width = av.getColumnSelection().findColumnPosition(width); } @@ -536,7 +607,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param evt - * DOCUMENT ME! + * DOCUMENT ME! */ public void adjustmentValueChanged(AdjustmentEvent evt) { @@ -548,9 +619,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { int x = hscroll.getValue(); av.setStartRes(x); - av - .setEndRes((x + (seqPanel.seqCanvas.getWidth() / av - .getCharWidth())) - 1); + av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1); } if (evt.getSource() == vscroll) @@ -633,8 +702,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (updateOverview) { - jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sequenceColoursChanged(this); + av.getStructureSelectionManager().sequenceColoursChanged(this); if (overviewPanel != null) { @@ -647,7 +715,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! */ public void paintComponent(Graphics g) { @@ -660,9 +728,9 @@ public class AlignmentPanel extends GAlignmentPanel implements if (av.getWrapAlignment()) { - int maxwidth = av.alignment.getWidth(); + int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } @@ -690,16 +758,16 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param pg - * DOCUMENT ME! + * DOCUMENT ME! * @param pf - * DOCUMENT ME! + * DOCUMENT ME! * @param pi - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! * * @throws PrinterException - * DOCUMENT ME! + * DOCUMENT ME! */ public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException @@ -723,23 +791,23 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param pg - * DOCUMENT ME! + * DOCUMENT ME! * @param pwidth - * DOCUMENT ME! + * DOCUMENT ME! * @param pheight - * DOCUMENT ME! + * DOCUMENT ME! * @param pi - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! * * @throws PrinterException - * DOCUMENT ME! + * DOCUMENT ME! */ public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException { - int idWidth = getVisibleIdWidth(); + int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); int scaleHeight = av.charHeight + fm.getDescent(); @@ -786,7 +854,8 @@ public class AlignmentPanel extends GAlignmentPanel implements endSeq = av.getAlignment().getHeight(); } - int pagesHigh = ((av.alignment.getHeight() / totalSeq) + 1) * pheight; + int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1) + * pheight; if (av.showAnnotation) { @@ -830,8 +899,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } pg.setColor(currentColor); - pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, av - .getCharHeight()); + pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, + av.getCharHeight()); pg.setColor(currentTextColor); @@ -844,7 +913,9 @@ public class AlignmentPanel extends GAlignmentPanel implements - 4; } - pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos, + pg.drawString( + seq.getDisplayId(av.getShowJVSuffix()), + xPos, (((i - startSeq) * av.charHeight) + av.getCharHeight()) - (av.getCharHeight() / 5)); } @@ -855,12 +926,17 @@ public class AlignmentPanel extends GAlignmentPanel implements pg.translate(idWidth, 0); seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0); - if (av.showAnnotation && (endSeq == av.alignment.getHeight())) + if (av.showAnnotation && (endSeq == av.getAlignment().getHeight())) { + // draw annotation - need to offset for current scroll position + int offset = -alabels.scrollOffset; + pg.translate(0, offset); pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3); alabels.drawComponent((Graphics2D) pg, idWidth); pg.translate(idWidth + 3, 0); - annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes + 1); + annotationPanel.renderer.drawComponent(annotationPanel, av, + (Graphics2D) pg, -1, startRes, endRes + 1); + pg.translate(0, -offset); } return Printable.PAGE_EXISTS; @@ -870,18 +946,18 @@ public class AlignmentPanel extends GAlignmentPanel implements * DOCUMENT ME! * * @param pg - * DOCUMENT ME! + * DOCUMENT ME! * @param pwidth - * DOCUMENT ME! + * DOCUMENT ME! * @param pheight - * DOCUMENT ME! + * DOCUMENT ME! * @param pi - * DOCUMENT ME! + * DOCUMENT ME! * * @return DOCUMENT ME! * * @throws PrinterException - * DOCUMENT ME! + * DOCUMENT ME! */ public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException @@ -904,10 +980,10 @@ public class AlignmentPanel extends GAlignmentPanel implements int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + annotationHeight; - int idWidth = getVisibleIdWidth(); + int idWidth = getVisibleIdWidth(false); - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } @@ -933,10 +1009,10 @@ public class AlignmentPanel extends GAlignmentPanel implements do { - for (int i = 0; i < av.alignment.getHeight(); i++) + for (int i = 0; i < av.getAlignment().getHeight(); i++) { pg.setFont(idPanel.idCanvas.idfont); - SequenceI s = av.alignment.getSequenceAt(i); + SequenceI s = av.getAlignment().getSequenceAt(i); String string = s.getDisplayId(av.getShowJVSuffix()); int xPos = 0; if (av.rightAlignIds) @@ -978,88 +1054,140 @@ public class AlignmentPanel extends GAlignmentPanel implements } } + /** + * get current sequence ID panel width, or nominal value if panel were to be + * displayed using default settings + * + * @return + */ int getVisibleIdWidth() { - return idPanel.getWidth() > 0 ? idPanel.getWidth() - : calculateIdWidth().width + 4; + return getVisibleIdWidth(true); } - void makeAlignmentImage(int type, File file) + /** + * get current sequence ID panel width, or nominal value if panel were to be + * displayed using default settings + * + * @param onscreen + * indicate if the Id width for onscreen or offscreen display should + * be returned + * @return + */ + int getVisibleIdWidth(boolean onscreen) { - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + // see if rendering offscreen - check preferences and calc width accordingly + if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false)) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); + return calculateIdWidth(-1).width + 4; } - - int height = ((av.alignment.getHeight() + 1) * av.charHeight) - + scalePanel.getHeight(); - int width = getVisibleIdWidth() + (maxwidth * av.charWidth); - - if (av.getWrapAlignment()) + Integer idwidth = null; + if (onscreen + || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) { - height = getWrappedHeight(); - if (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true")) - { - width = alignFrame.getWidth() - vscroll.getPreferredSize().width - - alignFrame.getInsets().left - - alignFrame.getInsets().right; - } - else - { - width = seqPanel.getWidth() + getVisibleIdWidth(); - } - + return (idPanel.getWidth() > 0 ? idPanel.getWidth() + : calculateIdWidth().width + 4); } - else if (av.getShowAnnotation()) + return idwidth.intValue() + 4; + } + + void makeAlignmentImage(int type, File file) + { + long progress = System.currentTimeMillis(); + if (alignFrame != null) { - height += annotationPanel.adjustPanelHeight() + 3; + alignFrame.setProgressBar("Saving " + + (type == jalview.util.ImageMaker.PNG ? "PNG image" + : "EPS file"), progress); } - try { - - jalview.util.ImageMaker im; - if (type == jalview.util.ImageMaker.PNG) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG, - "Create PNG image from alignment", width, height, file, - null); - } - else - { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, - "Create EPS file from alignment", width, height, file, - alignFrame.getTitle()); + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); } + int height = ((av.getAlignment().getHeight() + 1) * av.charHeight) + + scalePanel.getHeight(); + int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth); + if (av.getWrapAlignment()) { - if (im.getGraphics() != null) + height = getWrappedHeight(); + if (System.getProperty("java.awt.headless") != null + && System.getProperty("java.awt.headless").equals("true")) { - printWrappedAlignment(im.getGraphics(), width, height, 0); - im.writeImage(); + // need to obtain default alignment width and then add in any + // additional allowance for id margin + // this duplicates the calculation in getWrappedHeight but adjusts for + // offscreen idWith + width = alignFrame.getWidth() - vscroll.getPreferredSize().width + - alignFrame.getInsets().left + - alignFrame.getInsets().right - getVisibleIdWidth() + + getVisibleIdWidth(false); } + else + { + width = seqPanel.getWidth() + getVisibleIdWidth(false); + } + } - else + else if (av.getShowAnnotation()) + { + height += annotationPanel.adjustPanelHeight() + 3; + } + + try { - if (im.getGraphics() != null) + + jalview.util.ImageMaker im; + final String imageAction, imageTitle; + if (type == jalview.util.ImageMaker.PNG) { - printUnwrapped(im.getGraphics(), width, height, 0); - im.writeImage(); + imageAction = "Create PNG image from alignment"; + imageTitle = null; } + else + { + imageAction = "Create EPS file from alignment"; + imageTitle = alignFrame.getTitle(); + } + im = new jalview.util.ImageMaker(this, type, imageAction, width, + height, file, imageTitle); + if (av.getWrapAlignment()) + { + if (im.getGraphics() != null) + { + printWrappedAlignment(im.getGraphics(), width, height, 0); + im.writeImage(); + } + } + else + { + if (im.getGraphics() != null) + { + printUnwrapped(im.getGraphics(), width, height, 0); + im.writeImage(); + } + } + } catch (OutOfMemoryError err) + { + // Be noisy here. + System.out.println("########################\n" + "OUT OF MEMORY " + + file + "\n" + "########################"); + new OOMWarning("Creating Image for " + file, err); + // System.out.println("Create IMAGE: " + err); + } catch (Exception ex) + { + ex.printStackTrace(); } - } catch (OutOfMemoryError err) - { - // Be noisy here. - System.out.println("########################\n" + "OUT OF MEMORY " - + file + "\n" + "########################"); - new OOMWarning("Creating Image for " + file, err); - // System.out.println("Create IMAGE: " + err); - } catch (Exception ex) + } finally { - ex.printStackTrace(); + if (alignFrame != null) + { + alignFrame.setProgressBar("Export complete.", progress); + } } } @@ -1083,7 +1211,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS // //////////////////////////////////////////// - int idWidth = getVisibleIdWidth(); + int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); int scaleHeight = av.charHeight + fm.getDescent(); @@ -1093,8 +1221,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { try { - int s, sSize = av.alignment.getHeight(), res, alwidth = av.alignment - .getWidth(), g, gSize, f, fSize, sy; + int s, sSize = av.getAlignment().getHeight(), res, alwidth = av + .getAlignment().getWidth(), g, gSize, f, fSize, sy; StringBuffer text = new StringBuffer(); PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); out.println(jalview.io.HTMLOutput.getImageMapHTML()); @@ -1106,15 +1234,15 @@ public class AlignmentPanel extends GAlignmentPanel implements { sy = s * av.charHeight + scaleHeight; - SequenceI seq = av.alignment.getSequenceAt(s); + SequenceI seq = av.getAlignment().getSequenceAt(s); SequenceFeature[] features = seq.getDatasetSequence() .getSequenceFeatures(); - SequenceGroup[] groups = av.alignment.findAllGroups(seq); + SequenceGroup[] groups = av.getAlignment().findAllGroups(seq); for (res = 0; res < alwidth; res++) { text = new StringBuffer(); Object obj = null; - if (av.alignment.isNucleotide()) + if (av.getAlignment().isNucleotide()) { obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) + ""); @@ -1250,8 +1378,8 @@ public class AlignmentPanel extends GAlignmentPanel implements int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + annotationHeight; - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } @@ -1260,4 +1388,120 @@ public class AlignmentPanel extends GAlignmentPanel implements return height; } + + /** + * close the panel - deregisters all listeners and nulls any references to + * alignment data. + */ + public void closePanel() + { + PaintRefresher.RemoveComponent(seqPanel.seqCanvas); + PaintRefresher.RemoveComponent(idPanel.idCanvas); + PaintRefresher.RemoveComponent(this); + if (av != null) + { + jalview.structure.StructureSelectionManager ssm = av + .getStructureSelectionManager(); + ssm.removeStructureViewerListener(seqPanel, null); + ssm.removeSelectionListener(seqPanel); + av.setAlignment(null); + av = null; + } + else + { + if (Cache.log.isDebugEnabled()) + { + Cache.log.warn("Closing alignment panel which is already closed."); + } + } + } + + /** + * hides or shows dynamic annotation rows based on groups and av state flags + */ + public void updateAnnotation() + { + updateAnnotation(false, false); + } + + public void updateAnnotation(boolean applyGlobalSettings) + { + updateAnnotation(applyGlobalSettings, false); + } + + public void updateAnnotation(boolean applyGlobalSettings, + boolean preserveNewGroupSettings) + { + av.updateGroupAnnotationSettings(applyGlobalSettings, + preserveNewGroupSettings); + adjustAnnotationHeight(); + } + + @Override + public AlignmentI getAlignment() + { + return av.getAlignment(); + } + + /** + * get the name for this view + * + * @return + */ + public String getViewName() + { + return av.viewName; + } + + /** + * Make/Unmake this alignment panel the current input focus + * + * @param b + */ + public void setSelected(boolean b) + { + try + { + alignFrame.setSelected(b); + } catch (Exception ex) + { + } + ; + + if (b) + { + alignFrame.setDisplayedView(this); + } + } + + @Override + public StructureSelectionManager getStructureSelectionManager() + { + return av.getStructureSelectionManager(); + } + + @Override + public void raiseOOMWarning(String string, OutOfMemoryError error) + { + new OOMWarning(string, error, this); + } + + public FeatureRenderer cloneFeatureRenderer() + { + + return new FeatureRenderer(this); + } + + public void updateFeatureRenderer(FeatureRenderer fr) + { + fr.transferSettings(seqPanel.seqCanvas.getFeatureRenderer()); + } + + public void updateFeatureRendererFrom(FeatureRenderer fr) + { + if (seqPanel.seqCanvas.getFeatureRenderer() != null) + { + seqPanel.seqCanvas.getFeatureRenderer().transferSettings(fr); + } + } }