X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=541c7c29104d93a80632f0c8e65186ee86f7f1c6;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=4c8df4b2a4a2ec721135ec80e818aa9397a92838;hpb=9fa4caf83992b2c67feebe40e8015d984e1bb540;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 4c8df4b..541c7c2 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,26 +1,25 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors * * This file is part of Jalview. * * 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 Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; import java.beans.*; import java.io.*; -import java.util.Hashtable; -import java.util.Vector; import java.awt.*; import java.awt.event.*; @@ -174,16 +173,19 @@ 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 + * + * @param maxwidth + * -1 or maximum width allowed for IdWidth * @return Dimension giving the maximum width of the alignment label panel * that should be used. */ @@ -233,7 +235,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - return new Dimension(maxwidth<0 ? idWidth : Math.min(maxwidth, idWidth), 12); + return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth, + idWidth), 12); } /** @@ -283,8 +286,8 @@ public class AlignmentPanel extends GAlignmentPanel implements return false; } SequenceI seq = av.getAlignment().getSequenceAt(seqIndex); - - int[] r=results.getResults(seq, 0, av.getAlignment().getWidth()); + + int[] r = results.getResults(seq, 0, av.getAlignment().getWidth()); if (r == null) { return false; @@ -305,7 +308,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { start = av.getColumnSelection().findColumnPosition(start); end = av.getColumnSelection().findColumnPosition(end); - if (start==end) + if (start == end) { if (!av.getColumnSelection().isVisible(r[0])) { @@ -381,8 +384,9 @@ public class AlignmentPanel extends GAlignmentPanel implements /** * - * @param b Hide or show annotation panel - * + * @param b + * Hide or show annotation panel + * */ public void setAnnotationVisible(boolean b) { @@ -395,8 +399,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * automatically adjust annotation panel height for new annotation - * whilst ensuring the alignment is still visible. + * automatically adjust annotation panel height for new annotation whilst + * ensuring the alignment is still visible. */ public void adjustAnnotationHeight() { @@ -410,13 +414,15 @@ public class AlignmentPanel extends GAlignmentPanel implements addNotify(); paintAlignment(true); } + /** * calculate the annotation dimensions and refresh slider values accordingly. - * need to do repaints/notifys afterwards. + * need to do repaints/notifys afterwards. */ - protected void validateAnnotationDimensions(boolean adjustPanelHeight) { + protected void validateAnnotationDimensions(boolean adjustPanelHeight) + { int height = annotationPanel.adjustPanelHeight(); - + if (hscroll.isVisible()) { height += hscroll.getPreferredSize().height; @@ -428,10 +434,10 @@ public class AlignmentPanel extends GAlignmentPanel implements if (!adjustPanelHeight) { // maintain same window layout whilst updating sliders - height=annotationScroller.getSize().height; + height = annotationScroller.getSize().height; } hscroll.addNotify(); - + annotationScroller.setPreferredSize(new Dimension(annotationScroller .getWidth(), height)); @@ -538,10 +544,11 @@ public class AlignmentPanel extends GAlignmentPanel implements /** * Adjust row/column scrollers to show a visible position in the alignment. * - * @param x visible column to scroll to - * DOCUMENT ME! - * @param y visible row to scroll to - * + * @param x + * visible column to scroll to DOCUMENT ME! + * @param y + * visible row to scroll to + * */ public void setScrollValues(int x, int y) { @@ -682,7 +689,7 @@ public class AlignmentPanel extends GAlignmentPanel implements seqPanel.seqCanvas.fastPaint(scrollX, scrollY); scalePanel.repaint(); - if (av.getShowAnnotation()) + if (av.getShowAnnotation() && scrollX!=0) { annotationPanel.fastPaint(scrollX); } @@ -848,7 +855,8 @@ public class AlignmentPanel extends GAlignmentPanel implements endSeq = av.getAlignment().getHeight(); } - int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1) * pheight; + int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1) + * pheight; if (av.showAnnotation) { @@ -921,10 +929,15 @@ public class AlignmentPanel extends GAlignmentPanel implements 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.renderer.drawComponent(annotationPanel, av, (Graphics2D) pg, -1, startRes, endRes + 1); + annotationPanel.renderer.drawComponent(annotationPanel, av, + (Graphics2D) pg, -1, startRes, endRes + 1); + pg.translate(0, -offset); } return Printable.PAGE_EXISTS; @@ -1041,8 +1054,11 @@ public class AlignmentPanel extends GAlignmentPanel implements return Printable.NO_SUCH_PAGE; } } + /** - * get current sequence ID panel width, or nominal value if panel were to be displayed using default settings + * get current sequence ID panel width, or nominal value if panel were to be + * displayed using default settings + * * @return */ int getVisibleIdWidth() @@ -1051,8 +1067,12 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * 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 + * 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) @@ -1060,95 +1080,116 @@ public class AlignmentPanel extends GAlignmentPanel implements // see if rendering offscreen - check preferences and calc width accordingly if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false)) { - return calculateIdWidth(-1).width+4; + return calculateIdWidth(-1).width + 4; } - Integer idwidth=null; - if (onscreen || (idwidth=Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"))==null) { + Integer idwidth = null; + if (onscreen + || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) + { return (idPanel.getWidth() > 0 ? idPanel.getWidth() - : calculateIdWidth().width + 4); + : calculateIdWidth().width + 4); } - return idwidth.intValue()+4; + return idwidth.intValue() + 4; } void makeAlignmentImage(int type, File file) { - int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns()) - { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); + long progress = System.currentTimeMillis(); + boolean headless = (System.getProperty("java.awt.headless") != null + && System.getProperty("java.awt.headless").equals("true")); + if (alignFrame != null && !headless) + { + alignFrame.setProgressBar("Saving " + + (type == jalview.util.ImageMaker.PNG ? "PNG image" + : "EPS file"), progress); } - - int height = ((av.getAlignment().getHeight() + 1) * av.charHeight) - + scalePanel.getHeight(); - int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth); - - if (av.getWrapAlignment()) + try { - height = getWrappedHeight(); - if (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true")) - { - // 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 + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { - width = seqPanel.getWidth() + getVisibleIdWidth(false); + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); } - } - else if (av.getShowAnnotation()) - { - height += annotationPanel.adjustPanelHeight() + 3; - } - - try - { + int height = ((av.getAlignment().getHeight() + 1) * av.charHeight) + + scalePanel.getHeight(); + int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth); - jalview.util.ImageMaker im; - if (type == jalview.util.ImageMaker.PNG) + if (av.getWrapAlignment()) { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG, - "Create PNG image from alignment", width, height, file, - null); + height = getWrappedHeight(); + if (headless) + { + // 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()) { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, - "Create EPS file from alignment", width, height, file, - alignFrame.getTitle()); + height += annotationPanel.adjustPanelHeight() + 3; } - if (av.getWrapAlignment()) + try { - if (im.getGraphics() != null) + + jalview.util.ImageMaker im; + final String imageAction, imageTitle; + if (type == jalview.util.ImageMaker.PNG) { - printWrappedAlignment(im.getGraphics(), width, height, 0); - im.writeImage(); + imageAction = "Create PNG image from alignment"; + imageTitle = null; } - } - else - { - if (im.getGraphics() != 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 { - printUnwrapped(im.getGraphics(), width, height, 0); - im.writeImage(); + 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) + } finally { - // 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(); + if (alignFrame != null && !headless) + { + alignFrame.setProgressBar("Export complete.", progress); + } } } @@ -1182,8 +1223,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { try { - int s, sSize = av.getAlignment().getHeight(), res, alwidth = av.getAlignment() - .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()); @@ -1361,7 +1402,8 @@ public class AlignmentPanel extends GAlignmentPanel implements PaintRefresher.RemoveComponent(this); if (av != null) { - jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager(); + jalview.structure.StructureSelectionManager ssm = av + .getStructureSelectionManager(); ssm.removeStructureViewerListener(seqPanel, null); ssm.removeSelectionListener(seqPanel); av.setAlignment(null); @@ -1381,74 +1423,19 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void updateAnnotation() { - updateAnnotation(false); + updateAnnotation(false, false); } public void updateAnnotation(boolean applyGlobalSettings) { - // TODO: this should be merged with other annotation update stuff - that - // sits on AlignViewport - boolean updateCalcs = false; - boolean conv = av.isShowGroupConservation(); - boolean cons = av.isShowGroupConsensus(); - boolean showprf = av.isShowSequenceLogo(); - boolean showConsHist = av.isShowConsensusHistogram(); - boolean normLogo = av.isNormaliseSequenceLogo(); - - boolean sortg = true; - - // remove old automatic annotation - // add any new annotation - - Vector gr = av.getAlignment().getGroups(); // OrderedBy(av.getAlignment().getSequencesArray()); - // intersect alignment annotation with alignment groups + updateAnnotation(applyGlobalSettings, false); + } - AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation(); - Hashtable oldrfs = new Hashtable(); - if (aan != null) - { - for (int an = 0; an < aan.length; an++) - { - if (aan[an].autoCalculated && aan[an].groupRef != null) - { - oldrfs.put(aan[an].groupRef, aan[an].groupRef); - av.getAlignment().deleteAnnotation(aan[an]); - aan[an] = null; - } - } - } - SequenceGroup sg; - if (gr != null) - { - for (int g = 0; g < gr.size(); g++) - { - updateCalcs = false; - sg = (SequenceGroup) gr.elementAt(g); - if (applyGlobalSettings || !oldrfs.containsKey(sg)) - { - // set defaults for this group's conservation/consensus - sg.setshowSequenceLogo(showprf); - sg.setShowConsensusHistogram(showConsHist); - sg.setNormaliseSequenceLogo(normLogo); - } - if (conv) - { - updateCalcs = true; - av.getAlignment().addAnnotation(sg.getConservationRow(), 0); - } - if (cons) - { - updateCalcs = true; - av.getAlignment().addAnnotation(sg.getConsensus(), 0); - } - // refresh the annotation rows - if (updateCalcs) - { - sg.recalcConservation(); - } - } - } - oldrfs.clear(); + public void updateAnnotation(boolean applyGlobalSettings, + boolean preserveNewGroupSettings) + { + av.updateGroupAnnotationSettings(applyGlobalSettings, + preserveNewGroupSettings); adjustAnnotationHeight(); } @@ -1460,7 +1447,8 @@ public class AlignmentPanel extends GAlignmentPanel implements /** * get the name for this view - * @return + * + * @return */ public String getViewName() { @@ -1469,18 +1457,23 @@ public class AlignmentPanel extends GAlignmentPanel implements /** * Make/Unmake this alignment panel the current input focus + * * @param b */ public void setSelected(boolean b) { - try { + try + { alignFrame.setSelected(b); - } catch (Exception ex) {}; - + } catch (Exception ex) + { + } + ; + if (b) { alignFrame.setDisplayedView(this); - } + } } @Override @@ -1492,6 +1485,25 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override public void raiseOOMWarning(String string, OutOfMemoryError error) { - new OOMWarning(string, error, this); + 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); + } } }