X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=d8b0757c3fb187e8cb79332b425d1f1ea943bee7;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=0155a672df954c852bfa06d65360b29e31d6014f;hpb=299fbd01c9a02a8010cbba3885c1b958b15c16b2;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 0155a67..d8b0757 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,39 +1,58 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ 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. - * + * 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 . + * 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.*; -import java.awt.print.*; -import javax.swing.*; - +import jalview.analysis.AnnotationSorter; import jalview.api.AlignmentViewPanel; import jalview.bin.Cache; -import jalview.datamodel.*; -import jalview.jbgui.*; -import jalview.schemes.*; -import jalview.structure.SelectionSource; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.jbgui.GAlignmentPanel; +import jalview.math.AlignmentDimension; +import jalview.schemes.ResidueProperties; import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Container; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.event.AdjustmentEvent; +import java.awt.event.AdjustmentListener; +import java.awt.print.PageFormat; +import java.awt.print.Printable; +import java.awt.print.PrinterException; +import java.beans.PropertyChangeEvent; +import java.beans.PropertyChangeListener; +import java.io.File; +import java.io.FileWriter; +import java.io.PrintWriter; + +import javax.swing.SwingUtilities; /** * DOCUMENT ME! @@ -48,20 +67,21 @@ public class AlignmentPanel extends GAlignmentPanel implements OverviewPanel overviewPanel; - SeqPanel seqPanel; + private SeqPanel seqPanel; - IdPanel idPanel; + private IdPanel idPanel; + private boolean headless; IdwidthAdjuster idwidthAdjuster; /** DOCUMENT ME!! */ public AlignFrame alignFrame; - ScalePanel scalePanel; + private ScalePanel scalePanel; - AnnotationPanel annotationPanel; + private AnnotationPanel annotationPanel; - AnnotationLabels alabels; + private AnnotationLabels alabels; // this value is set false when selection area being dragged boolean fastPaint = true; @@ -82,27 +102,27 @@ public class AlignmentPanel extends GAlignmentPanel implements { alignFrame = af; this.av = av; - seqPanel = new SeqPanel(av, this); - idPanel = new IdPanel(av, this); + setSeqPanel(new SeqPanel(av, this)); + setIdPanel(new IdPanel(av, this)); - scalePanel = new ScalePanel(av, this); + setScalePanel(new ScalePanel(av, this)); - idPanelHolder.add(idPanel, BorderLayout.CENTER); + idPanelHolder.add(getIdPanel(), BorderLayout.CENTER); idwidthAdjuster = new IdwidthAdjuster(this); idSpaceFillerPanel1.add(idwidthAdjuster, BorderLayout.CENTER); - annotationPanel = new AnnotationPanel(this); - alabels = new AnnotationLabels(this); + setAnnotationPanel(new AnnotationPanel(this)); + setAlabels(new AnnotationLabels(this)); - annotationScroller.setViewportView(annotationPanel); - annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER); + annotationScroller.setViewportView(getAnnotationPanel()); + annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER); - scalePanelHolder.add(scalePanel, BorderLayout.CENTER); - seqPanelHolder.add(seqPanel, BorderLayout.CENTER); + scalePanelHolder.add(getScalePanel(), BorderLayout.CENTER); + seqPanelHolder.add(getSeqPanel(), BorderLayout.CENTER); setScrollValues(0, 0); - setAnnotationVisible(av.getShowAnnotation()); + setAnnotationVisible(av.isShowAnnotation()); hscroll.addAdjustmentListener(this); vscroll.addAdjustmentListener(this); @@ -148,13 +168,13 @@ public class AlignmentPanel extends GAlignmentPanel implements idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight + fm.getDescent())); - idPanel.idCanvas.gg = null; - seqPanel.seqCanvas.img = null; - annotationPanel.adjustPanelHeight(); + getIdPanel().getIdCanvas().gg = null; + getSeqPanel().seqCanvas.img = null; + getAnnotationPanel().adjustPanelHeight(); Dimension d = calculateIdWidth(); d.setSize(d.width + 4, d.height); - idPanel.idCanvas.setPreferredSize(d); + getIdPanel().getIdCanvas().setPreferredSize(d); hscrollFillerPanel.setPreferredSize(d); if (overviewPanel != null) @@ -175,16 +195,19 @@ 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)); + Math.min(afwidth - 200, 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. */ @@ -219,7 +242,7 @@ public class AlignmentPanel extends GAlignmentPanel implements if (al.getAlignmentAnnotation() != null) { - fm = c.getFontMetrics(alabels.getFont()); + fm = c.getFontMetrics(getAlabels().getFont()); while (i < al.getAlignmentAnnotation().length) { @@ -234,7 +257,8 @@ 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); } /** @@ -244,7 +268,7 @@ public class AlignmentPanel extends GAlignmentPanel implements public void highlightSearchResults(SearchResults results) { scrollToPosition(results); - seqPanel.seqCanvas.highlightSearchResults(results); + getSeqPanel().seqCanvas.highlightSearchResults(results); } /** @@ -276,16 +300,16 @@ 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; @@ -302,13 +326,13 @@ 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; @@ -349,8 +373,8 @@ public class AlignmentPanel extends GAlignmentPanel implements void scrollToWrappedVisible(int res) { - int cwidth = seqPanel.seqCanvas - .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); + int cwidth = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth)) { vscroll.setValue((res / cwidth)); @@ -382,8 +406,9 @@ 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) { @@ -396,8 +421,8 @@ 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() { @@ -411,28 +436,48 @@ 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) { - int height = annotationPanel.adjustPanelHeight(); - - if (hscroll.isVisible()) - { - height += hscroll.getPreferredSize().height; - } - if (height > alignFrame.getHeight() / 2) - { - height = alignFrame.getHeight() / 2; + protected void validateAnnotationDimensions(boolean adjustPanelHeight) + { + int height = getAnnotationPanel().adjustPanelHeight(); + + int theight = av.getCharHeight() + * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0 + : av.getAlignment().getHiddenSequences().getSize())); + float sscaling = (float) (theight / (1.0 * theight + height)); + float ascaling = (float) (height * 1.0 / alignFrame.getHeight()); + int rheight = alignFrame.getHeight() - height - av.getCharHeight(); + if (adjustPanelHeight) + { + // NOTE: this logic is different in the applet. Need a better algorithm to + // define behaviour + // try and set height according to alignment + if (ascaling > 0 && sscaling < 0.5) + { + // if the alignment is too big then + // default is 0.5 split + height = alignFrame.getHeight() / 2; + } + else + { + // if space for more than one sequence row left when annotation is fully + // displayed then set height to annotation height + // otherwise, leave at least two lines of sequence shown. + height = (rheight > av.getCharHeight()) ? height + : (-av.getCharHeight() * 3 + (int) (alignFrame.getHeight() * (1 - sscaling))); + } } - if (!adjustPanelHeight) + else { // maintain same window layout whilst updating sliders - height=annotationScroller.getSize().height; + height = annotationScroller.getSize().height; } hscroll.addNotify(); - + annotationScroller.setPreferredSize(new Dimension(annotationScroller .getWidth(), height)); @@ -460,7 +505,7 @@ public class AlignmentPanel extends GAlignmentPanel implements annotationScroller.setVisible(false); annotationSpaceFillerHolder.setVisible(false); } - else if (av.showAnnotation) + else if (av.isShowAnnotation()) { annotationScroller.setVisible(true); annotationSpaceFillerHolder.setVisible(true); @@ -539,30 +584,31 @@ 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); } - av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1); + av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av.charWidth)) - 1); - hextent = seqPanel.seqCanvas.getWidth() / av.charWidth; - vextent = seqPanel.seqCanvas.getHeight() / av.charHeight; + hextent = getSeqPanel().seqCanvas.getWidth() / av.charWidth; + vextent = getSeqPanel().seqCanvas.getHeight() / av.charHeight; if (hextent > width) { @@ -614,7 +660,7 @@ 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 + (getSeqPanel().seqCanvas.getWidth() / av.getCharWidth())) - 1); } if (evt.getSource() == vscroll) @@ -625,8 +671,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { if (offy > -1) { - int rowSize = seqPanel.seqCanvas - .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); + int rowSize = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); av.setStartRes(offy * rowSize); av.setEndRes((offy + 1) * rowSize); } @@ -648,7 +694,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { av.setStartSeq(offy); av.setEndSeq(offy - + (seqPanel.seqCanvas.getHeight() / av.getCharHeight())); + + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())); } } @@ -679,20 +725,29 @@ public class AlignmentPanel extends GAlignmentPanel implements if (scrollX != 0 || scrollY != 0) { - idPanel.idCanvas.fastPaint(scrollY); - seqPanel.seqCanvas.fastPaint(scrollX, scrollY); - scalePanel.repaint(); + getIdPanel().getIdCanvas().fastPaint(scrollY); + getSeqPanel().seqCanvas.fastPaint(scrollX, scrollY); + getScalePanel().repaint(); - if (av.getShowAnnotation()) + if (av.isShowAnnotation() && scrollX != 0) { - annotationPanel.fastPaint(scrollX); + getAnnotationPanel().fastPaint(scrollX); } } } } + /** + * Repaint the alignment including the annotations and overview panels (if + * shown). + */ public void paintAlignment(boolean updateOverview) { + final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), + av.isShowAutocalculatedAbove()); + sorter.sort(getAlignment() + .getAlignmentAnnotation(), + av.getSortAnnotationsBy()); repaint(); if (updateOverview) @@ -716,27 +771,27 @@ public class AlignmentPanel extends GAlignmentPanel implements { invalidate(); - Dimension d = idPanel.idCanvas.getPreferredSize(); + Dimension d = getIdPanel().getIdCanvas().getPreferredSize(); idPanelHolder.setPreferredSize(d); hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12)); validate(); 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; } - int canvasWidth = seqPanel.seqCanvas - .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); + int canvasWidth = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(getSeqPanel().seqCanvas.getWidth()); if (canvasWidth > 0) { int max = maxwidth - / seqPanel.seqCanvas - .getWrappedCanvasWidth(seqPanel.seqCanvas + / getSeqPanel().seqCanvas + .getWrappedCanvasWidth(getSeqPanel().seqCanvas .getWidth()) + 1; vscroll.setMaximum(max); vscroll.setUnitIncrement(1); @@ -814,7 +869,7 @@ public class AlignmentPanel extends GAlignmentPanel implements // / How many sequences and residues can we fit on a printable page? int totalRes = (pwidth - idWidth) / av.getCharWidth(); - int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) - 1; + int totalSeq = (pheight - scaleHeight) / av.getCharHeight() - 1; int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1; @@ -849,11 +904,12 @@ 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) + if (av.isShowAnnotation()) { - pagesHigh += annotationPanel.adjustPanelHeight() + 3; + pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3; } pagesHigh /= pheight; @@ -865,7 +921,7 @@ public class AlignmentPanel extends GAlignmentPanel implements // draw Scale pg.translate(idWidth, 0); - scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, + getScalePanel().drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight); pg.translate(-idWidth, scaleHeight); @@ -874,7 +930,7 @@ public class AlignmentPanel extends GAlignmentPanel implements Color currentColor = null; Color currentTextColor = null; - pg.setFont(idPanel.idCanvas.idfont); + pg.setFont(getIdPanel().getIdCanvas().getIdfont()); SequenceI seq; for (int i = startSeq; i < endSeq; i++) @@ -899,7 +955,7 @@ public class AlignmentPanel extends GAlignmentPanel implements pg.setColor(currentTextColor); int xPos = 0; - if (av.rightAlignIds) + if (av.isRightAlignIds()) { fm = pg.getFontMetrics(); xPos = idWidth @@ -918,14 +974,19 @@ public class AlignmentPanel extends GAlignmentPanel implements // draw main sequence panel pg.translate(idWidth, 0); - seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0); + getSeqPanel().seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0); - if (av.showAnnotation && (endSeq == av.alignment.getHeight())) + if (av.isShowAnnotation() && (endSeq == av.getAlignment().getHeight())) { + // draw annotation - need to offset for current scroll position + int offset = -getAlabels().getScrollOffset(); + pg.translate(0, offset); pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3); - alabels.drawComponent((Graphics2D) pg, idWidth); + getAlabels().drawComponent(pg, idWidth); pg.translate(idWidth + 3, 0); - annotationPanel.drawComponent((Graphics2D) pg, startRes, endRes + 1); + getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, + pg, -1, startRes, endRes + 1); + pg.translate(0, -offset); } return Printable.PAGE_EXISTS; @@ -954,9 +1015,9 @@ public class AlignmentPanel extends GAlignmentPanel implements int annotationHeight = 0; AnnotationLabels labels = null; - if (av.showAnnotation) + if (av.isShowAnnotation()) { - annotationHeight = annotationPanel.adjustPanelHeight(); + annotationHeight = getAnnotationPanel().adjustPanelHeight(); labels = new AnnotationLabels(av); } @@ -971,13 +1032,13 @@ public class AlignmentPanel extends GAlignmentPanel implements 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; } - int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth + int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth - idWidth); int totalHeight = cHeight * (maxwidth / resWidth + 1); @@ -998,13 +1059,13 @@ 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); + pg.setFont(getIdPanel().getIdCanvas().getIdfont()); + SequenceI s = av.getAlignment().getSequenceAt(i); String string = s.getDisplayId(av.getShowJVSuffix()); int xPos = 0; - if (av.rightAlignIds) + if (av.isRightAlignIds()) { FontMetrics fm = pg.getFontMetrics(); xPos = idWidth - fm.stringWidth(string) - 4; @@ -1029,7 +1090,7 @@ public class AlignmentPanel extends GAlignmentPanel implements pg.translate(idWidth, 0); - seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, + getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0); if ((pi * pheight) < totalHeight) @@ -1042,115 +1103,158 @@ 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() + public int getVisibleIdWidth() { 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 + * 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) + public 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; + 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); + Integer idwidth = null; + if (onscreen + || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) + { + return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth() + : calculateIdWidth().width + 4); + } + return idwidth.intValue() + 4; + } + + void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file) + { + long progress = 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 String[] + { type.getLabel() }), progress); + } + try + { + AlignmentDimension aDimension = getAlignmentDimension(); + try + { + jalview.util.ImageMaker im; + final String imageAction, imageTitle; + if (type == jalview.util.ImageMaker.TYPE.PNG) + { + imageAction = "Create PNG image from alignment"; + imageTitle = null; + } + else if (type == jalview.util.ImageMaker.TYPE.EPS) + { + imageAction = "Create EPS file from alignment"; + imageTitle = alignFrame.getTitle(); + } + else + { + imageAction = "Create SVG file from alignment"; + imageTitle = alignFrame.getTitle(); + } + + im = new jalview.util.ImageMaker(this, type, imageAction, + aDimension.getWidth(), aDimension.getHeight(), file, + imageTitle); + if (av.getWrapAlignment()) + { + if (im.getGraphics() != null) + { + printWrappedAlignment(im.getGraphics(), aDimension.getWidth(), + aDimension.getHeight(), 0); + im.writeImage(); + } + } + else + { + if (im.getGraphics() != null) + { + printUnwrapped(im.getGraphics(), aDimension.getWidth(), + aDimension.getHeight(), 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(); + } + } finally + { + if (alignFrame != null && !headless) + { + alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress); + } } - return idwidth.intValue()+4; } - void makeAlignmentImage(int type, File file) + public AlignmentDimension getAlignmentDimension() { - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); } - int height = ((av.alignment.getHeight() + 1) * av.charHeight) - + scalePanel.getHeight(); + int height = ((av.getAlignment().getHeight() + 1) * av.charHeight) + + getScalePanel().getHeight(); int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth); if (av.getWrapAlignment()) { height = getWrappedHeight(); - if (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true")) + 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 + // 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); + - alignFrame.getInsets().right - getVisibleIdWidth() + + getVisibleIdWidth(false); } else { - width = seqPanel.getWidth() + getVisibleIdWidth(false); + width = getSeqPanel().getWidth() + getVisibleIdWidth(false); } } - else if (av.getShowAnnotation()) + else if (av.isShowAnnotation()) { - height += annotationPanel.adjustPanelHeight() + 3; + height += getAnnotationPanel().adjustPanelHeight() + 3; } + return new AlignmentDimension(width, height); - try - { - - jalview.util.ImageMaker im; - 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()); - } - - 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(); - } } /** @@ -1158,7 +1262,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void makeEPS(File epsFile) { - makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile); + makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile); } /** @@ -1166,14 +1270,18 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void makePNG(File pngFile) { - makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile); + makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile); } + public void makeSVG(File svgFile) + { + makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile); + } public void makePNGImageMap(File imgMapFile, String imageName) { // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS // //////////////////////////////////////////// - int idWidth = getVisibleIdWidth(true); + int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); int scaleHeight = av.charHeight + fm.getDescent(); @@ -1183,8 +1291,8 @@ 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()); @@ -1196,15 +1304,15 @@ 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) + ""); @@ -1312,7 +1420,7 @@ public class AlignmentPanel extends GAlignmentPanel implements int getWrappedHeight() { - int seqPanelWidth = seqPanel.seqCanvas.getWidth(); + int seqPanelWidth = getSeqPanel().seqCanvas.getWidth(); if (System.getProperty("java.awt.headless") != null && System.getProperty("java.awt.headless").equals("true")) @@ -1322,7 +1430,7 @@ public class AlignmentPanel extends GAlignmentPanel implements - alignFrame.getInsets().left - alignFrame.getInsets().right; } - int chunkWidth = seqPanel.seqCanvas + int chunkWidth = getSeqPanel().seqCanvas .getWrappedCanvasWidth(seqPanelWidth); int hgap = av.charHeight; @@ -1332,16 +1440,16 @@ public class AlignmentPanel extends GAlignmentPanel implements } int annotationHeight = 0; - if (av.showAnnotation) + if (av.isShowAnnotation()) { - annotationHeight = annotationPanel.adjustPanelHeight(); + annotationHeight = getAnnotationPanel().adjustPanelHeight(); } 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; } @@ -1357,15 +1465,16 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void closePanel() { - PaintRefresher.RemoveComponent(seqPanel.seqCanvas); - PaintRefresher.RemoveComponent(idPanel.idCanvas); + PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas); + PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas()); PaintRefresher.RemoveComponent(this); if (av != null) { - jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager(); - ssm.removeStructureViewerListener(seqPanel, null); - ssm.removeSelectionListener(seqPanel); - av.alignment = null; + jalview.structure.StructureSelectionManager ssm = av + .getStructureSelectionManager(); + ssm.removeStructureViewerListener(getSeqPanel(), null); + ssm.removeSelectionListener(getSeqPanel()); + av.setAlignment(null); av = null; } else @@ -1382,85 +1491,30 @@ 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 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); - } - 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 - */ + + @Override public String getViewName() { return av.viewName; @@ -1468,18 +1522,23 @@ 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 @@ -1487,4 +1546,84 @@ public class AlignmentPanel extends GAlignmentPanel implements { return av.getStructureSelectionManager(); } + + @Override + public void raiseOOMWarning(String string, OutOfMemoryError error) + { + new OOMWarning(string, error, this); + } + + @Override + public jalview.api.FeatureRenderer cloneFeatureRenderer() + { + + return new FeatureRenderer(this); + } + @Override + public jalview.api.FeatureRenderer getFeatureRenderer() + { + return seqPanel.seqCanvas.getFeatureRenderer(); + } + public void updateFeatureRenderer(jalview.renderer.seqfeatures.FeatureRenderer fr) + { + fr.transferSettings(getSeqPanel().seqCanvas.getFeatureRenderer()); + } + + public void updateFeatureRendererFrom(jalview.api.FeatureRenderer fr) + { + if (getSeqPanel().seqCanvas.getFeatureRenderer() != null) + { + getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(fr); + } + } + + public ScalePanel getScalePanel() + { + return scalePanel; + } + + public void setScalePanel(ScalePanel scalePanel) + { + this.scalePanel = scalePanel; + } + + public SeqPanel getSeqPanel() + { + return seqPanel; + } + + public void setSeqPanel(SeqPanel seqPanel) + { + this.seqPanel = seqPanel; + } + + public AnnotationPanel getAnnotationPanel() + { + return annotationPanel; + } + + public void setAnnotationPanel(AnnotationPanel annotationPanel) + { + this.annotationPanel = annotationPanel; + } + + public AnnotationLabels getAlabels() + { + return alabels; + } + + public void setAlabels(AnnotationLabels alabels) + { + this.alabels = alabels; + } + + public IdPanel getIdPanel() + { + return idPanel; + } + + public void setIdPanel(IdPanel idPanel) + { + this.idPanel = idPanel; + } }