X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=190682941a129aca2ff76b5377fa7860c4c803a1;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=84e5efe56d5ff3e8bea4d9d856697ad176c1e634;hpb=5dc1f2c2e2827d06041127686c9f33ed1c06a31d;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java old mode 100755 new mode 100644 index 84e5efe..1906829 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,65 +1,92 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) + * Copyright (C) 2015 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.AlignViewportI; +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 jalview.util.Platform; + +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.Insets; +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 java.util.List; + +import javax.swing.SwingUtilities; /** * DOCUMENT ME! * * @author $author$ - * @version $Revision$ + * @version $Revision: 1.161 $ */ public class AlignmentPanel extends GAlignmentPanel implements - AdjustmentListener, Printable + AdjustmentListener, Printable, AlignmentViewPanel { public AlignViewport av; OverviewPanel overviewPanel; - SeqPanel seqPanel; + private SeqPanel seqPanel; + + private IdPanel idPanel; - 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; @@ -68,40 +95,42 @@ public class AlignmentPanel extends GAlignmentPanel implements int vextent = 0; + /* + * Flag set while scrolling to follow complementary cDNA/protein scroll. When + * true, suppresses invoking the same method recursively. + */ + private boolean followingComplementScroll; + /** * Creates a new AlignmentPanel object. * * @param af - * DOCUMENT ME! * @param av - * DOCUMENT ME! */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { 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()); - hscroll.addAdjustmentListener(this); vscroll.addAdjustmentListener(this); @@ -119,7 +148,13 @@ public class AlignmentPanel extends GAlignmentPanel implements }); fontChanged(); adjustAnnotationHeight(); + updateLayout(); + } + @Override + public AlignViewportI getAlignViewport() + { + return av; } public void alignmentChanged() @@ -141,24 +176,29 @@ public class AlignmentPanel extends GAlignmentPanel implements // to prevent drawing old image FontMetrics fm = getFontMetrics(av.getFont()); - scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight - + fm.getDescent())); - idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight + scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight() + fm.getDescent())); + idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av + .getCharHeight() + 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) { overviewPanel.setBoxPosition(); } + if (this.alignFrame.getSplitViewContainer() != null) + { + ((SplitFrame) this.alignFrame.getSplitViewContainer()).adjustLayout(); + } repaint(); } @@ -172,15 +212,41 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public Dimension calculateIdWidth() { + // calculate sensible default width when no preference is available + Dimension r = null; + if (av.getIdWidth() < 0) + { + int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); + int maxwidth = Math.max(20, Math.min(afwidth - 200, 2 * afwidth / 3)); + r = calculateIdWidth(maxwidth); + av.setIdWidth(r.width); + } + else + { + r = new Dimension(); + r.width = av.getIdWidth(); + r.height = 0; + } + return r; + } + + /** + * 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; @@ -204,7 +270,7 @@ 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) { @@ -219,71 +285,98 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - return new Dimension(Math.min(maxwidth, idWidth), 12); + return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth, + idWidth), 12); } /** - * DOCUMENT ME! + * Highlight the given results on the alignment. * - * @param results - * DOCUMENT ME! */ public void highlightSearchResults(SearchResults results) { scrollToPosition(results); - seqPanel.seqCanvas.highlightSearchResults(results); + getSeqPanel().seqCanvas.highlightSearchResults(results); } /** - * scroll the view to show the position of the highlighted region in results + * Scroll the view to show the position of the highlighted region in results * (if any) and redraw the overview * * @param results */ public boolean scrollToPosition(SearchResults results) { - return scrollToPosition(results, true); + return scrollToPosition(results, 0, true, false); } /** - * scroll the view to show the position of the highlighted region in results + * Scroll the view to show the position of the highlighted region in results + * (if any) + * + * @param searchResults + * @param redrawOverview + * @return + */ + public boolean scrollToPosition(SearchResults searchResults, + boolean redrawOverview) + { + return scrollToPosition(searchResults, 0, redrawOverview, false); + } + + /** + * Scroll the view to show the position of the highlighted region in results * (if any) * * @param results + * @param verticalOffset + * if greater than zero, allows scrolling to a position below the + * first displayed sequence * @param redrawOverview * - when set, the overview will be recalculated (takes longer) + * @param centre + * if true, try to centre the search results horizontally in the view * @return false if results were not found */ public boolean scrollToPosition(SearchResults results, - boolean redrawOverview) + int verticalOffset, boolean redrawOverview, boolean centre) { - int startv, endv, starts, ends, width; + int startv, endv, starts, ends; // TODO: properly locate search results in view when large numbers of hidden // columns exist before highlighted region // do we need to scroll the panel? - // TODO: tons of nullpointereexceptions raised here. + // TODO: tons of nullpointerexceptions 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()); // results.getResults(seq, - // seq.getStart(), - // seq.getEnd()); - // TODO: VAMSAS: fix hidden column issue where scroll to left from C - // terminus is not visible + int[] r = results.getResults(seq, 0, av.getAlignment().getWidth()); if (r == null) { return false; } int start = r[0]; int end = r[1]; - // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); // DEBUG + // DEBUG + // System.err.println(this.av.viewName + " Seq : " + seqIndex + // + " Scroll to " + start + "," + end); + + /* + * To centre results, scroll to positions half the visible width + * left/right of the start/end positions + */ + if (centre) + { + int offset = (av.getEndRes() - av.getStartRes() + 1) / 2 - 1; + start = Math.max(start - offset, 0); + end = end + offset - 1; + } if (start < 0) { return false; @@ -292,42 +385,81 @@ public class AlignmentPanel extends GAlignmentPanel implements { return false; } - if (!av.wrapAlignment) + if (av.hasHiddenColumns()) + { + start = av.getColumnSelection().findColumnPosition(start); + end = av.getColumnSelection().findColumnPosition(end); + if (start == end) + { + if (!av.getColumnSelection().isVisible(r[0])) + { + // don't scroll - position isn't visible + return false; + } + } + } + + /* + * allow for offset of target sequence (actually scroll to one above it) + */ + seqIndex = Math.max(0, seqIndex - verticalOffset); + + // System.out.println("start=" + start + ", end=" + end + ", startv=" + // + av.getStartRes() + ", endv=" + av.getEndRes() + ", starts=" + // + av.getStartSeq() + ", ends=" + av.getEndSeq()); + if (!av.getWrapAlignment()) { if ((startv = av.getStartRes()) >= start) { - setScrollValues(start - 1, seqIndex); + /* + * Scroll left to make start of search results visible + */ + // setScrollValues(start - 1, seqIndex); // plus one residue + setScrollValues(start, seqIndex); } else if ((endv = av.getEndRes()) <= end) { - setScrollValues(startv + 1 + end - endv, seqIndex); + /* + * Scroll right to make end of search results visible + */ + // setScrollValues(startv + 1 + end - endv, seqIndex); // plus one + setScrollValues(startv + end - endv, seqIndex); } else if ((starts = av.getStartSeq()) > seqIndex) { + /* + * Scroll up to make start of search results visible + */ setScrollValues(av.getStartRes(), seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) { + /* + * Scroll down to make end of search results visible + */ setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); } + /* + * Else results are already visible - no need to scroll + */ } else { scrollToWrappedVisible(start); } } - if (!redrawOverview && overviewPanel != null) + if (redrawOverview && overviewPanel != null) { overviewPanel.setBoxPosition(); } - paintAlignment(!redrawOverview); + paintAlignment(redrawOverview); return true; } 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)); @@ -358,14 +490,14 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! * * @param b - * DOCUMENT ME! + * Hide or show annotation panel + * */ public void setAnnotationVisible(boolean b) { - if (!av.wrapAlignment) + if (!av.getWrapAlignment()) { annotationSpaceFillerHolder.setVisible(b); annotationScroller.setVisible(b); @@ -373,6 +505,10 @@ 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 @@ -381,38 +517,72 @@ public class AlignmentPanel extends GAlignmentPanel implements { System.out.println("NEEDS FIXING"); } + validateAnnotationDimensions(true); + addNotify(); + paintAlignment(true); + } - int height = annotationPanel.adjustPanelHeight(); - - if (hscroll.isVisible()) - { - height += hscroll.getPreferredSize().height; + /** + * calculate the annotation dimensions and refresh slider values accordingly. + * need to do repaints/notifys afterwards. + */ + protected void validateAnnotationDimensions(boolean adjustPanelHeight) + { + int annotationHeight = getAnnotationPanel().adjustPanelHeight(); + + if (adjustPanelHeight) + { + int rowHeight = av.getCharHeight(); + int alignmentHeight = rowHeight * av.getAlignment().getHeight(); + + /* + * Estimate available height in the AlignFrame for alignment + + * annotations. Deduct an estimate for title bar, menu bar, scale panel, + * hscroll, status bar (as these are not laid out we can't inspect their + * actual heights). Insets gives frame borders. + */ + int stuff = Platform.isAMac() ? 80 : 100; + Insets insets = alignFrame.getInsets(); + int availableHeight = alignFrame.getHeight() - stuff - insets.top + - insets.bottom; + + /* + * If not enough vertical space, maximize annotation height while keeping + * at least two rows of alignment visible + */ + if (annotationHeight + alignmentHeight > availableHeight) + { + annotationHeight = Math.min(annotationHeight, availableHeight - 2 + * rowHeight); + } } - if (height > alignFrame.getHeight() / 2) + else { - height = alignFrame.getHeight() / 2; + // maintain same window layout whilst updating sliders + annotationHeight = annotationScroller.getSize().height; } - hscroll.addNotify(); annotationScroller.setPreferredSize(new Dimension(annotationScroller - .getWidth(), height)); + .getWidth(), annotationHeight)); annotationSpaceFillerHolder.setPreferredSize(new Dimension( - annotationSpaceFillerHolder.getWidth(), height)); - annotationScroller.validate();// repaint(); - addNotify(); - repaint(); + annotationSpaceFillerHolder.getWidth(), annotationHeight)); + annotationScroller.validate(); + annotationScroller.addNotify(); } /** - * DOCUMENT ME! + * update alignment layout for viewport settings * * @param wrap * DOCUMENT ME! */ - public void setWrapAlignment(boolean wrap) + public void updateLayout() { + fontChanged(); + setAnnotationVisible(av.isShowAnnotation()); + boolean wrap = av.getWrapAlignment(); av.startSeq = 0; scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); @@ -423,7 +593,7 @@ 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); @@ -500,32 +670,34 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * DOCUMENT ME! + * Adjust row/column scrollers to show a visible position in the alignment. * * @param x - * DOCUMENT ME! + * visible column to scroll to * @param y - * DOCUMENT ME! + * 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) + // System.err.println("Scroll " + this.av.viewName + " to " + x + "," + y); + if (av == null || av.getAlignment() == null) { return; } - int width = av.alignment.getWidth(); - int height = av.alignment.getHeight(); + int width = av.getAlignment().getWidth(); + int height = av.getAlignment().getHeight(); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { width = av.getColumnSelection().findColumnPosition(width); } - av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1); + av.setEndRes((x + (getSeqPanel().seqCanvas.getWidth() / av + .getCharWidth())) - 1); - hextent = seqPanel.seqCanvas.getWidth() / av.charWidth; - vextent = seqPanel.seqCanvas.getHeight() / av.charHeight; + hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); + vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); if (hextent > width) { @@ -569,7 +741,6 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void adjustmentValueChanged(AdjustmentEvent evt) { - int oldX = av.getStartRes(); int oldY = av.getStartSeq(); @@ -577,9 +748,8 @@ 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) @@ -590,8 +760,8 @@ 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); } @@ -613,7 +783,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { av.setStartSeq(offy); av.setEndSeq(offy - + (seqPanel.seqCanvas.getHeight() / av.getCharHeight())); + + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())); } } @@ -644,26 +814,46 @@ 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); } } } + /* + * If there is one, scroll the (Protein/cDNA) complementary alignment to + * match, unless we are ourselves doing that. + */ + if (isFollowingComplementScroll()) + { + setFollowingComplementScroll(false); + } + else + { + av.scrollComplementaryAlignment(); + } } + /** + * 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) { - jalview.structure.StructureSelectionManager - .getStructureSelectionManager().sequenceColoursChanged(this); + // TODO: determine if this paintAlignment changed structure colours + av.getStructureSelectionManager().sequenceColoursChanged(this); if (overviewPanel != null) { @@ -682,27 +872,27 @@ 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); @@ -768,9 +958,9 @@ 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(); + int scaleHeight = av.getCharHeight() + fm.getDescent(); pg.setColor(Color.white); pg.fillRect(0, 0, pwidth, pheight); @@ -780,7 +970,7 @@ 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; @@ -815,11 +1005,12 @@ 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; @@ -831,7 +1022,7 @@ 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); @@ -840,7 +1031,7 @@ 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++) @@ -859,13 +1050,13 @@ public class AlignmentPanel extends GAlignmentPanel implements } pg.setColor(currentColor); - pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, av - .getCharHeight()); + pg.fillRect(0, (i - startSeq) * av.getCharHeight(), idWidth, + av.getCharHeight()); pg.setColor(currentTextColor); int xPos = 0; - if (av.rightAlignIds) + if (av.isRightAlignIds()) { fm = pg.getFontMetrics(); xPos = idWidth @@ -874,7 +1065,7 @@ public class AlignmentPanel extends GAlignmentPanel implements } pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), xPos, - (((i - startSeq) * av.charHeight) + av.getCharHeight()) + (((i - startSeq) * av.getCharHeight()) + av.getCharHeight()) - (av.getCharHeight() / 5)); } @@ -882,14 +1073,21 @@ 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())) { - pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3); - alabels.drawComponent((Graphics2D) pg, idWidth); + // draw annotation - need to offset for current scroll position + int offset = -getAlabels().getScrollOffset(); + pg.translate(0, offset); + pg.translate(-idWidth - 3, (endSeq - startSeq) * av.getCharHeight() + + 3); + 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; @@ -915,33 +1113,32 @@ public class AlignmentPanel extends GAlignmentPanel implements public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, int pi) throws PrinterException { - int annotationHeight = 0; AnnotationLabels labels = null; - if (av.showAnnotation) + if (av.isShowAnnotation()) { - annotationHeight = annotationPanel.adjustPanelHeight(); + annotationHeight = getAnnotationPanel().adjustPanelHeight(); labels = new AnnotationLabels(av); } - int hgap = av.charHeight; - if (av.scaleAboveWrapped) + int hgap = av.getCharHeight(); + if (av.getScaleAboveWrapped()) { - hgap += av.charHeight; + hgap += av.getCharHeight(); } - int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + 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; } - int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth + int resWidth = getSeqPanel().seqCanvas.getWrappedCanvasWidth(pwidth - idWidth); int totalHeight = cHeight * (maxwidth / resWidth + 1); @@ -962,30 +1159,33 @@ 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; } pg.drawString(string, xPos, - ((i * av.charHeight) + ypos + av.charHeight) - - (av.charHeight / 5)); + ((i * av.getCharHeight()) + ypos + av.getCharHeight()) + - (av.getCharHeight() / 5)); } if (labels != null) { - pg.translate(-3, ypos - + (av.getAlignment().getHeight() * av.charHeight)); + pg.translate(-3, + ypos + (av.getAlignment().getHeight() * av.getCharHeight())); pg.setFont(av.getFont()); labels.drawComponent(pg, idWidth); - pg.translate(+3, -ypos - - (av.getAlignment().getHeight() * av.charHeight)); + pg.translate( + +3, + -ypos + - (av.getAlignment().getHeight() * av + .getCharHeight())); } ypos += cHeight; @@ -993,8 +1193,8 @@ public class AlignmentPanel extends GAlignmentPanel implements pg.translate(idWidth, 0); - seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, - 0); + getSeqPanel().seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, + totalHeight, 0); if ((pi * pheight) < totalHeight) { @@ -1007,89 +1207,158 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - int getVisibleIdWidth() + /** + * get current sequence ID panel width, or nominal value if panel were to be + * displayed using default settings + * + * @return + */ + public 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 + */ + public 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; } + Integer idwidth = null; + if (onscreen + || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) + { + return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth() + : calculateIdWidth().width + 4); + } + return idwidth.intValue() + 4; + } - int height = ((av.alignment.getHeight() + 1) * av.charHeight) - + scalePanel.getHeight(); - int width = getVisibleIdWidth() + (maxwidth * av.charWidth); - - if (av.getWrapAlignment()) + 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 Object[] { type.getLabel() }), + progress); + } + try { - height = getWrappedHeight(); - if (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true")) + AlignmentDimension aDimension = getAlignmentDimension(); + try { - width = alignFrame.getWidth() - vscroll.getPreferredSize().width - - alignFrame.getInsets().left - - alignFrame.getInsets().right; + 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(); } - else + } finally + { + if (alignFrame != null && !headless) { - width = seqPanel.getWidth() + getVisibleIdWidth(); + alignFrame.setProgressBar( + MessageManager.getString("status.export_complete"), + progress); } - } - else if (av.getShowAnnotation()) + } + + public AlignmentDimension getAlignmentDimension() + { + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { - height += annotationPanel.adjustPanelHeight() + 3; + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); } - try - { + int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) + + getScalePanel().getHeight(); + int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth()); - jalview.util.ImageMaker im; - if (type == jalview.util.ImageMaker.PNG) + if (av.getWrapAlignment()) + { + height = getWrappedHeight(); + if (headless) { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG, - "Create PNG image from alignment", width, height, file, - null); + // 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 { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, - "Create EPS file from alignment", width, height, file, - alignFrame.getTitle()); + width = getSeqPanel().getWidth() + getVisibleIdWidth(false); } - 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) + } + else if (av.isShowAnnotation()) { - ex.printStackTrace(); + height += getAnnotationPanel().adjustPanelHeight() + 3; } + return new AlignmentDimension(width, height); + } /** @@ -1097,7 +1366,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void makeEPS(File epsFile) { - makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile); + makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile); } /** @@ -1105,16 +1374,21 @@ 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(); + int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); - int scaleHeight = av.charHeight + fm.getDescent(); + int scaleHeight = av.getCharHeight() + fm.getDescent(); // Gen image map // //////////////////////////////// @@ -1122,8 +1396,8 @@ 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()); @@ -1133,33 +1407,31 @@ public class AlignmentPanel extends GAlignmentPanel implements for (s = 0; s < sSize; s++) { - sy = s * av.charHeight + scaleHeight; + sy = s * av.getCharHeight() + scaleHeight; - SequenceI seq = av.alignment.getSequenceAt(s); - SequenceFeature[] features = seq.getDatasetSequence() - .getSequenceFeatures(); - SequenceGroup[] groups = av.alignment.findAllGroups(seq); + SequenceI seq = av.getAlignment().getSequenceAt(s); + SequenceFeature[] features = seq.getSequenceFeatures(); + SequenceGroup[] groups = av.getAlignment().findAllGroups(seq); for (res = 0; res < alwidth; res++) { text = new StringBuffer(); - Object obj = null; - if (av.alignment.isNucleotide()) + String triplet = null; + if (av.getAlignment().isNucleotide()) { - obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) - + ""); + triplet = ResidueProperties.nucleotideName.get(seq + .getCharAt(res) + ""); } else { - obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res) + triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(res) + ""); } - if (obj == null) + if (triplet == null) { continue; } - String triplet = obj.toString(); int alIndex = seq.findPosition(res); gSize = groups.length; for (g = 0; g < gSize; g++) @@ -1167,9 +1439,9 @@ public class AlignmentPanel extends GAlignmentPanel implements if (text.length() < 1) { text.append(" seqs = av.getAlignment().getSequences(); + + /* + * This is like AlignmentI.findIndex(seq) but here we are matching the + * dataset sequence not the aligned sequence + */ + boolean matched = false; + for (SequenceI seq : seqs) + { + if (mappedTo == seq.getDatasetSequence()) { - sg.recalcConservation(); + matched = true; + break; } } + if (!matched) + { + return; // failsafe, shouldn't happen } - oldrfs.clear(); - adjustAnnotationHeight(); + + /* + * Scroll to position but centring the target residue. + */ + scrollToPosition(sr, verticalOffset, true, true); + } + + /** + * Set a flag to say we are scrolling to follow a (cDNA/protein) complement. + * + * @param b + */ + protected void setFollowingComplementScroll(boolean b) + { + this.followingComplementScroll = b; + } + + protected boolean isFollowingComplementScroll() + { + return this.followingComplementScroll; } }