X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=541c7c29104d93a80632f0c8e65186ee86f7f1c6;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=2b4c0dbc3fbc34eb84b6d225dcbc401d790c985f;hpb=bbfdb203ce3a889600caa52478478b75ab03809f;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 2b4c0db..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.*; @@ -32,7 +31,6 @@ import jalview.bin.Cache; import jalview.datamodel.*; import jalview.jbgui.*; import jalview.schemes.*; -import jalview.structure.SelectionSource; import jalview.structure.StructureSelectionManager; /** @@ -174,15 +172,31 @@ 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; @@ -221,7 +235,8 @@ 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); } /** @@ -263,16 +278,16 @@ public class AlignmentPanel extends GAlignmentPanel implements // do we need to scroll the panel? // TODO: tons of nullpointereexceptions raised here. if (results != null && results.getSize() > 0 && av != null - && av.alignment != null) + && av.getAlignment() != null) { - int seqIndex = av.alignment.findIndex(results); + int seqIndex = av.getAlignment().findIndex(results); if (seqIndex == -1) { return false; } - SequenceI seq = av.alignment.getSequenceAt(seqIndex); - - int[] r=results.getResults(seq, 0, av.alignment.getWidth()); + SequenceI seq = av.getAlignment().getSequenceAt(seqIndex); + + int[] r = results.getResults(seq, 0, av.getAlignment().getWidth()); if (r == null) { return false; @@ -289,13 +304,13 @@ public class AlignmentPanel extends GAlignmentPanel implements { return false; } - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { start = av.getColumnSelection().findColumnPosition(start); end = av.getColumnSelection().findColumnPosition(end); - if (start==end) + if (start == end) { - if (!av.colSel.isVisible(r[0])) + if (!av.getColumnSelection().isVisible(r[0])) { // don't scroll - position isn't visible return false; @@ -369,8 +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) { @@ -383,8 +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() { @@ -398,13 +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; @@ -416,10 +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)); @@ -526,22 +544,23 @@ 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) { // System.err.println("Scroll to "+x+","+y); - if (av == null || av.alignment == null) + 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); } @@ -670,7 +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); } @@ -710,9 +729,9 @@ 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; } @@ -789,7 +808,7 @@ public class AlignmentPanel extends GAlignmentPanel implements 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(); @@ -836,7 +855,8 @@ 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) { @@ -907,12 +927,17 @@ 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; @@ -956,10 +981,10 @@ 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; } @@ -985,10 +1010,10 @@ 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) @@ -1030,89 +1055,141 @@ 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")) - { - // TODO: JAL-244 - width = alignFrame.getWidth() - vscroll.getPreferredSize().width - - alignFrame.getInsets().left - - alignFrame.getInsets().right; - } - else - { - width = seqPanel.getWidth() + getVisibleIdWidth(); - } - - } - else if (av.getShowAnnotation()) - { - height += annotationPanel.adjustPanelHeight() + 3; + return (idPanel.getWidth() > 0 ? idPanel.getWidth() + : calculateIdWidth().width + 4); } + return idwidth.intValue() + 4; + } + void makeAlignmentImage(int type, File file) + { + 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); + } 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 (headless) { - 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) + { + 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()) { - printUnwrapped(im.getGraphics(), width, height, 0); - im.writeImage(); + 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 && !headless) + { + alignFrame.setProgressBar("Export complete.", progress); + } } } @@ -1136,7 +1213,7 @@ 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(); @@ -1146,8 +1223,8 @@ 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()); @@ -1159,15 +1236,15 @@ 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) + ""); @@ -1303,8 +1380,8 @@ 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; } @@ -1325,10 +1402,11 @@ 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.alignment = null; + av.setAlignment(null); av = null; } else @@ -1345,86 +1423,32 @@ 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.alignment.getGroups(); // OrderedBy(av.alignment.getSequencesArray()); - // intersect alignment annotation with alignment groups + updateAnnotation(applyGlobalSettings, false); + } - AlignmentAnnotation[] aan = av.alignment.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.alignment.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.alignment.addAnnotation(sg.getConservationRow(), 0); - } - if (cons) - { - updateCalcs = true; - av.alignment.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(); } @Override public AlignmentI getAlignment() { - return av.alignment; + return av.getAlignment(); } /** * get the name for this view - * @return + * + * @return */ public String getViewName() { @@ -1433,18 +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 @@ -1452,4 +1481,29 @@ public class AlignmentPanel extends GAlignmentPanel implements { 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); + } + } }