X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=851c58b8ccb3e5fef4accf80290a8d50e7957ad6;hb=9612728299dc4c2242a6a968875a194624983920;hp=74f691168e6a293dd40d198b7bb0e2dbd47dd864;hpb=f9eda693703846de8930781126d6c07a119dde73;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java old mode 100755 new mode 100644 index 74f6911..851c58b --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,65 +1,89 @@ /* - * 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 ($$Version-Rel$$) + * 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 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 java.util.List; + +import javax.swing.SwingUtilities; + +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; /** * 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; - 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; @@ -68,40 +92,42 @@ 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); @@ -119,9 +145,14 @@ public class AlignmentPanel extends GAlignmentPanel implements }); fontChanged(); adjustAnnotationHeight(); - + updateLayout(); } + @Override + public AlignViewportI getAlignViewport() + { + return av; + } public void alignmentChanged() { av.alignmentChanged(this); @@ -141,24 +172,30 @@ public class AlignmentPanel extends GAlignmentPanel implements // to prevent drawing old image FontMetrics fm = getFontMetrics(av.getFont()); - scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight + scalePanelHolder.setPreferredSize(new Dimension(10, av.getCharHeight() + fm.getDescent())); - idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight + 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 +209,41 @@ 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 +267,7 @@ 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) { @@ -219,7 +282,8 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - return new Dimension(Math.min(maxwidth, idWidth), 12); + return new Dimension(maxwidth < 0 ? idWidth : Math.min(maxwidth, + idWidth), 12); } /** @@ -229,48 +293,63 @@ public class AlignmentPanel extends GAlignmentPanel implements 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, true, false); + } + + /** + * 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, redrawOverview, 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 results * @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) + 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. 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; @@ -279,6 +358,17 @@ public class AlignmentPanel extends GAlignmentPanel implements int end = r[1]; // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); // // DEBUG + + /* + * 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 = Math.min(end + offset, seq.getEnd() - 1); + } if (start < 0) { return false; @@ -287,37 +377,52 @@ 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; } } } - if (!av.wrapAlignment) + if (!av.getWrapAlignment()) { if ((startv = av.getStartRes()) >= start) { + /* + * Scroll left to make start of search results visible + */ setScrollValues(start - 1, seqIndex); } else if ((endv = av.getEndRes()) <= end) { + /* + * Scroll right to make end of search results visible + */ setScrollValues(startv + 1 + 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 { @@ -334,8 +439,8 @@ 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)); @@ -366,14 +471,14 @@ 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); @@ -381,6 +486,10 @@ 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 @@ -389,18 +498,50 @@ public class AlignmentPanel extends GAlignmentPanel implements { System.out.println("NEEDS FIXING"); } + validateAnnotationDimensions(true); + addNotify(); + paintAlignment(true); + } - int height = annotationPanel.adjustPanelHeight(); - - if (hscroll.isVisible()) + /** + * calculate the annotation dimensions and refresh slider values accordingly. + * need to do repaints/notifys afterwards. + */ + 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) { - height += hscroll.getPreferredSize().height; + // 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 (height > alignFrame.getHeight() / 2) + else { - height = alignFrame.getHeight() / 2; + // maintain same window layout whilst updating sliders + height = annotationScroller.getSize().height; } - hscroll.addNotify(); annotationScroller.setPreferredSize(new Dimension(annotationScroller @@ -409,18 +550,20 @@ public class AlignmentPanel extends GAlignmentPanel implements annotationSpaceFillerHolder.setPreferredSize(new Dimension( annotationSpaceFillerHolder.getWidth(), height)); annotationScroller.validate();// repaint(); - addNotify(); - repaint(); + 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); @@ -431,7 +574,7 @@ 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); @@ -510,30 +653,32 @@ 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 + .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) { @@ -577,7 +722,6 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void adjustmentValueChanged(AdjustmentEvent evt) { - int oldX = av.getStartRes(); int oldY = av.getStartSeq(); @@ -585,7 +729,7 @@ 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) @@ -596,8 +740,8 @@ 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); } @@ -619,7 +763,7 @@ public class AlignmentPanel extends GAlignmentPanel implements { av.setStartSeq(offy); av.setEndSeq(offy - + (seqPanel.seqCanvas.getHeight() / av.getCharHeight())); + + (getSeqPanel().seqCanvas.getHeight() / av.getCharHeight())); } } @@ -650,26 +794,46 @@ 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(evt.getSource() == hscroll); + } } + /** + * 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); + av.getStructureSelectionManager().sequenceColoursChanged(this); if (overviewPanel != null) { @@ -688,27 +852,27 @@ 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); @@ -774,9 +938,9 @@ 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); @@ -786,7 +950,7 @@ 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; @@ -821,11 +985,12 @@ 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; @@ -837,7 +1002,7 @@ 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); @@ -846,7 +1011,7 @@ 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++) @@ -865,13 +1030,13 @@ public class AlignmentPanel extends GAlignmentPanel implements } pg.setColor(currentColor); - pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, + 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 @@ -882,7 +1047,7 @@ 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)); } @@ -890,14 +1055,20 @@ 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; @@ -923,33 +1094,32 @@ 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); @@ -970,30 +1140,31 @@ 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)); + + (av.getAlignment().getHeight() * av.getCharHeight())); pg.setFont(av.getFont()); labels.drawComponent(pg, idWidth); pg.translate(+3, -ypos - - (av.getAlignment().getHeight() * av.charHeight)); + - (av.getAlignment().getHeight() * av + .getCharHeight())); } ypos += cHeight; @@ -1001,7 +1172,7 @@ 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) @@ -1015,89 +1186,156 @@ 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; } - - int height = ((av.alignment.getHeight() + 1) * av.charHeight) - + scalePanel.getHeight(); - int width = getVisibleIdWidth() + (maxwidth * av.charWidth); - - if (av.getWrapAlignment()) + Integer idwidth = null; + if (onscreen + || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) { - height = getWrappedHeight(); - if (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true")) - { - width = alignFrame.getWidth() - vscroll.getPreferredSize().width - - alignFrame.getInsets().left - - alignFrame.getInsets().right; - } - else - { - width = seqPanel.getWidth() + getVisibleIdWidth(); - } - + return (getIdPanel().getWidth() > 0 ? getIdPanel().getWidth() + : calculateIdWidth().width + 4); } - else if (av.getShowAnnotation()) + 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) { - height += annotationPanel.adjustPanelHeight() + 3; + alignFrame.setProgressBar(MessageManager.formatMessage( + "status.saving_file", new Object[] + { 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(); + } - jalview.util.ImageMaker im; - if (type == jalview.util.ImageMaker.PNG) + 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) { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG, - "Create PNG image from alignment", width, height, file, - null); + // 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) { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, - "Create EPS file from alignment", width, height, file, - alignFrame.getTitle()); + alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress); } + } + } - if (av.getWrapAlignment()) + public AlignmentDimension getAlignmentDimension() + { + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) + { + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); + } + + int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) + + getScalePanel().getHeight(); + int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth()); + + if (av.getWrapAlignment()) + { + height = getWrappedHeight(); + if (headless) { - if (im.getGraphics() != null) - { - printWrappedAlignment(im.getGraphics(), width, height, 0); - im.writeImage(); - } + // need to obtain default alignment width and then add in any + // additional allowance for id margin + // this duplicates the calculation in getWrappedHeight but adjusts for + // offscreen idWith + width = alignFrame.getWidth() - vscroll.getPreferredSize().width + - alignFrame.getInsets().left + - alignFrame.getInsets().right - getVisibleIdWidth() + + getVisibleIdWidth(false); } else { - if (im.getGraphics() != null) - { - printUnwrapped(im.getGraphics(), width, height, 0); - im.writeImage(); - } + width = getSeqPanel().getWidth() + getVisibleIdWidth(false); } - } 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); + } /** @@ -1105,7 +1343,7 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void makeEPS(File epsFile) { - makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile); + makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile); } /** @@ -1113,16 +1351,20 @@ 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 // //////////////////////////////// @@ -1130,8 +1372,8 @@ 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()); @@ -1141,33 +1383,32 @@ 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++) @@ -1175,9 +1416,10 @@ 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 + */ + int sequenceIndex = 0; + boolean matched = false; + for (SequenceI seq : seqs) + { + if (mappedTo == seq.getDatasetSequence()) { - 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(); - } + matched = true; + break; } + sequenceIndex++; } - oldrfs.clear(); - adjustAnnotationHeight(); + if (!matched) + { + return; // failsafe, shouldn't happen + } + sequenceIndex = Math.max(0, sequenceIndex - seqOffset); + sr.getResults().get(0) + .setSequence(av.getAlignment().getSequenceAt(sequenceIndex)); + + /* + * Scroll to position but centring the target residue. Also set a state flag + * to prevent adjustmentValueChanged performing this recursively. + */ + setFollowingComplementScroll(true); + scrollToPosition(sr, 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; } }