X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=8f2dd04fc8bdd8683bc5e2fe80fb8df8f188932b;hb=3eef76298c55f3def21eed2516b5ace4405bed0a;hp=d06251c7694de626e8dd9140ec6475f5986e7475;hpb=ecf2d49dbf1d62c024845715f141a596cff8b065;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java old mode 100755 new mode 100644 index d06251c..8f2dd04 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * 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 * * This file is part of Jalview. * @@ -20,27 +20,27 @@ package jalview.gui; import java.beans.*; import java.io.*; import java.util.Hashtable; -import java.util.Vector; import java.awt.*; 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; @@ -172,15 +172,28 @@ 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; @@ -219,7 +232,7 @@ 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); } /** @@ -261,16 +274,16 @@ 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); + SequenceI seq = av.getAlignment().getSequenceAt(seqIndex); - int[] r=results.getResults(seq, 0, av.alignment.getWidth()); + int[] r=results.getResults(seq, 0, av.getAlignment().getWidth()); if (r == null) { return false; @@ -287,13 +300,13 @@ 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 (!av.colSel.isVisible(r[0])) + if (!av.getColumnSelection().isVisible(r[0])) { // don't scroll - position isn't visible return false; @@ -324,11 +337,11 @@ public class AlignmentPanel extends GAlignmentPanel implements scrollToWrappedVisible(start); } } - if (!redrawOverview && overviewPanel != null) + if (redrawOverview && overviewPanel != null) { overviewPanel.setBoxPosition(); } - paintAlignment(!redrawOverview); + paintAlignment(redrawOverview); return true; } @@ -366,10 +379,9 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! * - * @param b - * DOCUMENT ME! + * @param b Hide or show annotation panel + * */ public void setAnnotationVisible(boolean b) { @@ -381,6 +393,10 @@ 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 @@ -389,9 +405,17 @@ 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()) { height += hscroll.getPreferredSize().height; @@ -400,17 +424,20 @@ 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 .getWidth(), height)); annotationSpaceFillerHolder.setPreferredSize(new Dimension( annotationSpaceFillerHolder.getWidth(), height)); annotationScroller.validate();// repaint(); - addNotify(); - repaint(); + annotationScroller.addNotify(); } /** @@ -518,14 +545,14 @@ public class AlignmentPanel extends GAlignmentPanel implements 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); } @@ -668,8 +695,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (updateOverview) { - jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sequenceColoursChanged(this); + av.getStructureSelectionManager().sequenceColoursChanged(this); if (overviewPanel != null) { @@ -695,9 +721,9 @@ 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; } @@ -774,7 +800,7 @@ 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(); @@ -821,7 +847,7 @@ 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) { @@ -892,12 +918,16 @@ 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; @@ -941,10 +971,10 @@ 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; } @@ -970,10 +1000,10 @@ 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) @@ -1014,24 +1044,51 @@ 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 + * @return + */ int getVisibleIdWidth() { - return idPanel.getWidth() > 0 ? idPanel.getWidth() - : calculateIdWidth().width + 4; + return getVisibleIdWidth(true); + } + + /** + * 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) + { + // see if rendering offscreen - check preferences and calc width accordingly + if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false)) + { + return calculateIdWidth(-1).width+4; + } + Integer idwidth=null; + if (onscreen || (idwidth=Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"))==null) { + return (idPanel.getWidth() > 0 ? idPanel.getWidth() + : calculateIdWidth().width + 4); + } + return idwidth.intValue()+4; } void makeAlignmentImage(int type, File file) { - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + long progress=System.currentTimeMillis(); + if (alignFrame!=null) { + alignFrame.setProgressBar("Saving "+(type == jalview.util.ImageMaker.PNG ? "PNG image":"EPS file") , progress); + } + try { + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); } - int height = ((av.alignment.getHeight() + 1) * av.charHeight) + int height = ((av.getAlignment().getHeight() + 1) * av.charHeight) + scalePanel.getHeight(); - int width = getVisibleIdWidth() + (maxwidth * av.charWidth); + int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth); if (av.getWrapAlignment()) { @@ -1039,13 +1096,16 @@ public class AlignmentPanel extends GAlignmentPanel implements 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; + - alignFrame.getInsets().right + - getVisibleIdWidth()+getVisibleIdWidth(false); } else { - width = seqPanel.getWidth() + getVisibleIdWidth(); + width = seqPanel.getWidth() + getVisibleIdWidth(false); } } @@ -1058,19 +1118,17 @@ public class AlignmentPanel extends GAlignmentPanel implements { jalview.util.ImageMaker im; + final String imageAction,imageTitle; if (type == jalview.util.ImageMaker.PNG) { - 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()); + 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) @@ -1098,6 +1156,13 @@ public class AlignmentPanel extends GAlignmentPanel implements { ex.printStackTrace(); } + } + finally { + if (alignFrame!=null) + { + alignFrame.setProgressBar("Export complete.", progress); + } + } } /** @@ -1120,7 +1185,7 @@ 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(); @@ -1130,7 +1195,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { try { - int s, sSize = av.alignment.getHeight(), res, alwidth = av.alignment + 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)); @@ -1143,15 +1208,15 @@ 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) + ""); @@ -1287,8 +1352,8 @@ 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; } @@ -1304,16 +1369,15 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void closePanel() { - jalview.structure.StructureSelectionManager ssm = jalview.structure.StructureSelectionManager - .getStructureSelectionManager(); - ssm.removeStructureViewerListener(seqPanel, null); - ssm.removeSelectionListener(seqPanel); PaintRefresher.RemoveComponent(seqPanel.seqCanvas); PaintRefresher.RemoveComponent(idPanel.idCanvas); PaintRefresher.RemoveComponent(this); if (av != null) { - av.alignment = null; + jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager(); + ssm.removeStructureViewerListener(seqPanel, null); + ssm.removeSelectionListener(seqPanel); + av.setAlignment(null); av = null; } else @@ -1342,16 +1406,16 @@ public class AlignmentPanel extends GAlignmentPanel implements 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 - AlignmentAnnotation[] aan = av.alignment.getAlignmentAnnotation(); + AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation(); Hashtable oldrfs = new Hashtable(); if (aan != null) { @@ -1360,33 +1424,32 @@ public class AlignmentPanel extends GAlignmentPanel implements if (aan[an].autoCalculated && aan[an].groupRef != null) { oldrfs.put(aan[an].groupRef, aan[an].groupRef); - av.alignment.deleteAnnotation(aan[an]); + av.getAlignment().deleteAnnotation(aan[an]); aan[an] = null; } } } - SequenceGroup sg; - if (gr != null) + if (av.getAlignment().getGroups()!=null) { - for (int g = 0; g < gr.size(); g++) + for (SequenceGroup sg:av.getAlignment().getGroups()) { 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); + av.getAlignment().addAnnotation(sg.getConservationRow(), 0); } if (cons) { updateCalcs = true; - av.alignment.addAnnotation(sg.getConsensus(), 0); + av.getAlignment().addAnnotation(sg.getConsensus(), 0); } // refresh the annotation rows if (updateCalcs) @@ -1398,4 +1461,65 @@ public class AlignmentPanel extends GAlignmentPanel implements oldrfs.clear(); 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); + } + } }