X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=58aa645eb156091058a019476feadd7fb32a8e85;hb=2639d90e2b52d49cf586c0b602bc606033c9b8ae;hp=95b4220fa53ee60410c2b3d23f2a80f20ac046dd;hpb=8dd1cd955b1c6f1a89afc2068ab1cdfca3824934;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java old mode 100755 new mode 100644 index 95b4220..58aa645 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,124 +1,215 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 + * 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. - * - * This program 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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.awt.*; -import java.awt.event.*; -import java.awt.print.*; -import javax.swing.*; - -import jalview.datamodel.*; -import jalview.jbgui.*; -import jalview.schemes.*; +import jalview.analysis.AnnotationSorter; +import jalview.api.AlignViewportI; +import jalview.api.AlignmentViewPanel; +import jalview.bin.Cache; +import jalview.bin.Jalview; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.HiddenColumns; +import jalview.datamodel.SearchResultsI; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.gui.ImageExporter.ImageWriterI; +import jalview.io.HTMLOutput; +import jalview.jbgui.GAlignmentPanel; +import jalview.math.AlignmentDimension; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureSelectionManager; +import jalview.util.Comparison; +import jalview.util.ImageMaker; +import jalview.util.MessageManager; +import jalview.util.Platform; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; + +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.event.ComponentAdapter; +import java.awt.event.ComponentEvent; +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 +public class AlignmentPanel extends GAlignmentPanel implements + AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI { public AlignViewport av; + OverviewPanel overviewPanel; - SeqPanel seqPanel; - IdPanel idPanel; + + private SeqPanel seqPanel; + + private IdPanel idPanel; + IdwidthAdjuster idwidthAdjuster; - /** DOCUMENT ME!! */ public AlignFrame alignFrame; - ScalePanel scalePanel; - AnnotationPanel annotationPanel; - AnnotationLabels alabels; - // this value is set false when selection area being dragged - boolean fastPaint = true; - int hextent = 0; - int vextent = 0; + private ScalePanel scalePanel; + + private AnnotationPanel annotationPanel; + + private AnnotationLabels alabels; + + private int hextent = 0; + + private int vextent = 0; + + /* + * Flag set while scrolling to follow complementary cDNA/protein scroll. When + * false, suppresses invoking the same method recursively. + */ + private boolean scrollComplementaryPanel = true; + + private PropertyChangeListener propertyChangeListener; + + private CalculationChooser calculationDialog; /** * Creates a new AlignmentPanel object. - * - * @param af DOCUMENT ME! - * @param av DOCUMENT ME! + * + * @param af + * @param av */ 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); + addComponentListener(new ComponentAdapter() + { + @Override + public void componentResized(ComponentEvent evt) + { + // reset the viewport ranges when the alignment panel is resized + // in particular, this initialises the end residue value when Jalview + // is initialised + ViewportRanges ranges = av.getRanges(); + if (av.getWrapAlignment()) + { + int widthInRes = getSeqPanel().seqCanvas.getWrappedCanvasWidth( + getSeqPanel().seqCanvas.getWidth()); + ranges.setViewportWidth(widthInRes); + } + else + { + int widthInRes = getSeqPanel().seqCanvas.getWidth() + / av.getCharWidth(); + int heightInSeq = getSeqPanel().seqCanvas.getHeight() + / av.getCharHeight(); + + ranges.setViewportWidth(widthInRes); + ranges.setViewportHeight(heightInSeq); + } + } + + }); + final AlignmentPanel ap = this; - av.addPropertyChangeListener(new PropertyChangeListener() + propertyChangeListener = new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) { - PaintRefresher.Refresh(ap, - av.getSequenceSetId(), - true, - true); + PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true); alignmentChanged(); } } - }); + }; + av.addPropertyChangeListener(propertyChangeListener); + av.getRanges().addPropertyChangeListener(this); fontChanged(); adjustAnnotationHeight(); + updateLayout(); + } + @Override + public AlignViewportI getAlignViewport() + { + return av; } public void alignmentChanged() { av.alignmentChanged(this); + if (getCalculationDialog() != null) + { + getCalculationDialog().validateCalcTypes(); + } + alignFrame.updateEditMenuBar(); - paintAlignment(true); + // no idea if we need to update structure + paintAlignment(true, true); } @@ -131,48 +222,74 @@ public class AlignmentPanel // 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 + fm.getDescent())); - - idPanel.idCanvas.gg = null; - seqPanel.seqCanvas.img = null; - annotationPanel.adjustPanelHeight(); + scalePanelHolder.setPreferredSize( + new Dimension(10, av.getCharHeight() + fm.getDescent())); + idSpaceFillerPanel1.setPreferredSize( + new Dimension(10, av.getCharHeight() + fm.getDescent())); + idwidthAdjuster.invalidate(); + scalePanelHolder.invalidate(); + 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(); - } - repaint(); } /** - * Calculate the width of the alignment labels based on the displayed names and any bounds on label width set in preferences. - * - * @return Dimension giving the maximum width of the alignment label panel that should be used. + * Calculate the width of the alignment labels based on the displayed names + * and any bounds on label width set in preferences. + * + * @return Dimension giving the maximum width of the alignment label panel + * that should be used. */ 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())); + 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; - while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null)) + while ((i < al.getHeight()) && (al.getSequenceAt(i) != null)) { SequenceI s = al.getSequenceAt(i); @@ -191,7 +308,7 @@ public class AlignmentPanel if (al.getAlignmentAnnotation() != null) { - fm = c.getFontMetrics(alabels.getFont()); + fm = c.getFontMetrics(getAlabels().getFont()); while (i < al.getAlignmentAnnotation().length) { @@ -206,57 +323,168 @@ public class AlignmentPanel } } - return new Dimension(Math.min(maxwidth, idWidth), 12); + return new Dimension( + maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12); } /** - * DOCUMENT ME! - * - * @param results DOCUMENT ME! + * Highlight the given results on the alignment. + * + */ + public void highlightSearchResults(SearchResultsI results) + { + boolean scrolled = scrollToPosition(results, 0, true, false); + + boolean fastPaint = !(scrolled && av.getWrapAlignment()); + + getSeqPanel().seqCanvas.highlightSearchResults(results, fastPaint); + } + + /** + * Scroll the view to show the position of the highlighted region in results + * (if any) + * + * @param searchResults + * @param redrawOverview + * @return */ - public void highlightSearchResults(SearchResults results) + public boolean scrollToPosition(SearchResultsI searchResults, + boolean redrawOverview) { - seqPanel.seqCanvas.highlightSearchResults(results); + return scrollToPosition(searchResults, 0, redrawOverview, false); + } - // do we need to scroll the panel? - if (results != null) + /** + * Scrolls the view (if necessary) to show the position of the first + * highlighted region in results (if any). Answers true if the view was + * scrolled, or false if no matched region was found, or it is already + * visible. + * + * @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 + */ + protected boolean scrollToPosition(SearchResultsI results, + int verticalOffset, boolean redrawOverview, boolean centre) + { + int startv, endv, starts, ends; + ViewportRanges ranges = av.getRanges(); + + if (results == null || results.isEmpty() || av == null + || av.getAlignment() == null) + { + return false; + } + int seqIndex = av.getAlignment().findIndex(results); + if (seqIndex == -1) + { + return false; + } + SequenceI seq = av.getAlignment().getSequenceAt(seqIndex); + + int[] r = results.getResults(seq, 0, av.getAlignment().getWidth()); + if (r == null) { - SequenceI seq = results.getResultSequence(0); - int seqIndex = av.alignment.findIndex(seq); - int start = seq.findIndex(results.getResultStart(0)) - 1; - int end = seq.findIndex(results.getResultEnd(0)) - 1; + return false; + } + int start = r[0]; + int end = r[1]; + + /* + * To centre results, scroll to positions half the visible width + * left/right of the start/end positions + */ + if (centre) + { + int offset = (ranges.getEndRes() - ranges.getStartRes() + 1) / 2 - 1; + start = Math.max(start - offset, 0); + end = end + offset - 1; + } + if (start < 0) + { + return false; + } + if (end == seq.getEnd()) + { + return false; + } - if (!av.wrapAlignment) + if (av.hasHiddenColumns()) + { + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + start = hidden.absoluteToVisibleColumn(start); + end = hidden.absoluteToVisibleColumn(end); + if (start == end) { - if ( (av.getStartRes() > end) || (av.getEndRes() < start) || - ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex))) + if (!hidden.isVisible(r[0])) { - setScrollValues(start, seqIndex); + // don't scroll - position isn't visible + return false; } } - else - { - scrollToWrappedVisible(start); - } } - paintAlignment(true); - } + /* + * allow for offset of target sequence (actually scroll to one above it) + */ + seqIndex = Math.max(0, seqIndex - verticalOffset); + boolean scrollNeeded = true; - void scrollToWrappedVisible(int res) - { - int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas. - getWidth()); - if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth)) + if (!av.getWrapAlignment()) + { + if ((startv = ranges.getStartRes()) >= start) + { + /* + * Scroll left to make start of search results visible + */ + setScrollValues(start, seqIndex); + } + else if ((endv = ranges.getEndRes()) <= end) + { + /* + * Scroll right to make end of search results visible + */ + setScrollValues(startv + end - endv, seqIndex); + } + else if ((starts = ranges.getStartSeq()) > seqIndex) + { + /* + * Scroll up to make start of search results visible + */ + setScrollValues(ranges.getStartRes(), seqIndex); + } + else if ((ends = ranges.getEndSeq()) <= seqIndex) + { + /* + * Scroll down to make end of search results visible + */ + setScrollValues(ranges.getStartRes(), starts + seqIndex - ends + + 1); + } + /* + * Else results are already visible - no need to scroll + */ + scrollNeeded = false; + } + else { - vscroll.setValue(res / cwidth); - av.startRes = vscroll.getValue() * cwidth; + scrollNeeded = ranges.scrollToWrappedVisible(start); } + + paintAlignment(redrawOverview, false); + + return scrollNeeded; } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public OverviewPanel getOverviewPanel() @@ -266,8 +494,9 @@ public class AlignmentPanel /** * DOCUMENT ME! - * - * @param op DOCUMENT ME! + * + * @param op + * DOCUMENT ME! */ public void setOverviewPanel(OverviewPanel op) { @@ -275,13 +504,14 @@ public class AlignmentPanel } /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param b + * Hide or show annotation panel + * */ public void setAnnotationVisible(boolean b) { - if (!av.wrapAlignment) + if (!av.getWrapAlignment()) { annotationSpaceFillerHolder.setVisible(b); annotationScroller.setVisible(b); @@ -289,47 +519,89 @@ public class AlignmentPanel repaint(); } + /** + * automatically adjust annotation panel height for new annotation whilst + * ensuring the alignment is still visible. + */ + @Override public void adjustAnnotationHeight() { - //TODO: display vertical annotation scrollbar if necessary + // TODO: display vertical annotation scrollbar if necessary // this is called after loading new annotation onto alignment if (alignFrame.getHeight() == 0) { System.out.println("NEEDS FIXING"); } + validateAnnotationDimensions(true); + addNotify(); + // TODO: many places call this method and also paintAlignment with various + // different settings. this means multiple redraws are triggered... + paintAlignment(true, false); + } - int height = annotationPanel.adjustPanelHeight(); + /** + * 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 (hscroll.isVisible()) + if (adjustPanelHeight) { - height += hscroll.getPreferredSize().height; + 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, insets. + */ + int stuff = Platform.isAMac() ? 120 : 140; + int availableHeight = alignFrame.getHeight() - stuff; + + /* + * 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)); + new Dimension(annotationScroller.getWidth(), annotationHeight)); + Dimension e = idPanel.getSize(); + alabels.setSize(new Dimension(e.width, annotationHeight)); annotationSpaceFillerHolder.setPreferredSize(new Dimension( - annotationSpaceFillerHolder.getWidth(), - height)); - annotationScroller.validate();// repaint(); - repaint(); + annotationSpaceFillerHolder.getWidth(), annotationHeight)); + annotationScroller.validate(); + annotationScroller.addNotify(); } /** - * DOCUMENT ME! - * - * @param wrap DOCUMENT ME! + * update alignment layout for viewport settings + * + * @param wrap + * DOCUMENT ME! */ - public void setWrapAlignment(boolean wrap) + public void updateLayout() { - av.startSeq = 0; + fontChanged(); + setAnnotationVisible(av.isShowAnnotation()); + boolean wrap = av.getWrapAlignment(); + ViewportRanges ranges = av.getRanges(); + ranges.setStartSeq(0); scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); idwidthAdjuster.setVisible(!wrap); @@ -339,239 +611,248 @@ public class AlignmentPanel annotationScroller.setVisible(false); annotationSpaceFillerHolder.setVisible(false); } - else if (av.showAnnotation) + else if (av.isShowAnnotation()) { annotationScroller.setVisible(true); annotationSpaceFillerHolder.setVisible(true); } + int canvasWidth = getSeqPanel().seqCanvas.getWidth(); + if (canvasWidth > 0) + { // may not yet be laid out + if (wrap) + { + int widthInRes = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(canvasWidth); + ranges.setViewportWidth(widthInRes); + } + else + { + int widthInRes = (canvasWidth / av.getCharWidth()); + int heightInSeq = (getSeqPanel().seqCanvas.getHeight() + / av.getCharHeight()); + + ranges.setViewportWidth(widthInRes); + ranges.setViewportHeight(heightInSeq); + } + } + idSpaceFillerPanel1.setVisible(!wrap); repaint(); } - // return value is true if the scroll is valid - public boolean scrollUp(boolean up) + /** + * Adjust row/column scrollers to show a visible position in the alignment. + * + * @param x + * visible column to scroll to + * @param y + * visible row to scroll to + * + */ + public void setScrollValues(int xpos, int ypos) { - if (up) + int x = xpos; + int y = ypos; + + if (av == null || av.getAlignment() == null) { - if (vscroll.getValue() < 1) - { - return false; - } + return; + } - fastPaint = false; - vscroll.setValue(vscroll.getValue() - 1); + if (av.getWrapAlignment()) + { + setScrollingForWrappedPanel(x); } else { - if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight()) + int width = av.getAlignment().getWidth(); + int height = av.getAlignment().getHeight(); + + if (av.hasHiddenColumns()) { - return false; + // reset the width to exclude hidden columns + width = av.getAlignment().getHiddenColumns() + .absoluteToVisibleColumn(width); } - fastPaint = false; - vscroll.setValue(vscroll.getValue() + 1); - } + hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); + vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); - fastPaint = true; + if (hextent > width) + { + hextent = width; + } - return true; - } + if (vextent > height) + { + vextent = height; + } - /** - * DOCUMENT ME! - * - * @param right DOCUMENT ME! - * - * @return DOCUMENT ME! - */ - public boolean scrollRight(boolean right) - { - if (!right) - { - if (hscroll.getValue() < 1) + if ((hextent + x) > width) { - return false; + x = width - hextent; } - fastPaint = false; - hscroll.setValue(hscroll.getValue() - 1); - } - else - { - if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth()) + if ((vextent + y) > height) { - return false; + y = height - vextent; } - fastPaint = false; - hscroll.setValue(hscroll.getValue() + 1); - } + if (y < 0) + { + y = 0; + } - fastPaint = true; + if (x < 0) + { + x = 0; + } - return true; + // update the scroll values + hscroll.setValues(x, hextent, 0, width); + vscroll.setValues(y, vextent, 0, height); + } } /** - * DOCUMENT ME! - * - * @param x DOCUMENT ME! - * @param y DOCUMENT ME! + * Respond to adjustment event when horizontal or vertical scrollbar is + * changed + * + * @param evt + * adjustment event encoding whether hscroll or vscroll changed */ - public void setScrollValues(int x, int y) + @Override + public void adjustmentValueChanged(AdjustmentEvent evt) { - - int width = av.alignment.getWidth(); - int height = av.alignment.getHeight(); - - if (av.hasHiddenColumns) - { - width = av.getColumnSelection().findColumnPosition(width); - } - - av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1); - - hextent = seqPanel.seqCanvas.getWidth() / av.charWidth; - vextent = seqPanel.seqCanvas.getHeight() / av.charHeight; - - if (hextent > width) + if (av.getWrapAlignment()) { - hextent = width; + adjustScrollingWrapped(evt); + return; } - if (vextent > height) - { - vextent = height; - } + ViewportRanges ranges = av.getRanges(); - if ( (hextent + x) > width) - { - x = width - hextent; - } - - if ( (vextent + y) > height) + if (evt.getSource() == hscroll) { - y = height - vextent; - } + int oldX = ranges.getStartRes(); + int oldwidth = ranges.getViewportWidth(); + int x = hscroll.getValue(); + int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); - if (y < 0) - { - y = 0; + // if we're scrolling to the position we're already at, stop + // this prevents infinite recursion of events when the scroll/viewport + // ranges values are the same + if ((x == oldX) && (width == oldwidth)) + { + return; + } + ranges.setViewportStartAndWidth(x, width); } - - if (x < 0) + else if (evt.getSource() == vscroll) { - x = 0; + int oldY = ranges.getStartSeq(); + int oldheight = ranges.getViewportHeight(); + int y = vscroll.getValue(); + int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); + + // if we're scrolling to the position we're already at, stop + // this prevents infinite recursion of events when the scroll/viewport + // ranges values are the same + if ((y == oldY) && (height == oldheight)) + { + return; + } + ranges.setViewportStartAndHeight(y, height); } - - hscroll.setValues(x, hextent, 0, width); - vscroll.setValues(y, vextent, 0, height); + repaint(); } /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * Responds to a scroll change by setting the start position of the viewport. + * Does + * + * @param evt */ - public void adjustmentValueChanged(AdjustmentEvent evt) + protected void adjustScrollingWrapped(AdjustmentEvent evt) { - - int oldX = av.getStartRes(); - int oldY = av.getStartSeq(); - if (evt.getSource() == hscroll) { - int x = hscroll.getValue(); - av.setStartRes(x); - av.setEndRes( (x + - (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1); + return; // no horizontal scroll when wrapped } + final ViewportRanges ranges = av.getRanges(); if (evt.getSource() == vscroll) { - int offy = vscroll.getValue(); - - if (av.getWrapAlignment()) + int newY = vscroll.getValue(); + + /* + * if we're scrolling to the position we're already at, stop + * this prevents infinite recursion of events when the scroll/viewport + * ranges values are the same + */ + int oldX = ranges.getStartRes(); + int oldY = ranges.getWrappedScrollPosition(oldX); + if (oldY == newY) { - if (offy > -1) - { - int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel. - seqCanvas.getWidth()); - av.setStartRes(offy * rowSize); - av.setEndRes( (offy + 1) * rowSize); - } - else - { - //This is only called if file loaded is a jar file that - //was wrapped when saved and user has wrap alignment true - //as preference setting - SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - setScrollValues(av.getStartRes(), av.getStartSeq()); - } - }); - } + return; } - else + if (newY > -1) { - av.setStartSeq(offy); - av.setEndSeq(offy + - (seqPanel.seqCanvas.getHeight() / av.getCharHeight())); + /* + * limit page up/down to one width's worth of positions + */ + int rowSize = ranges.getViewportWidth(); + int newX = newY > oldY ? oldX + rowSize : oldX - rowSize; + ranges.setViewportStartAndWidth(Math.max(0, newX), rowSize); } } - - if (overviewPanel != null) - { - overviewPanel.setBoxPosition(); - } - - int scrollX = av.startRes - oldX; - int scrollY = av.startSeq - oldY; - - if (av.getWrapAlignment() || !fastPaint) - { - repaint(); - } else { - // Make sure we're not trying to draw a panel - // larger than the visible window - if (scrollX > av.endRes - av.startRes) - { - scrollX = av.endRes - av.startRes; - } - else if (scrollX < av.startRes - av.endRes) + // This is only called if file loaded is a jar file that + // was wrapped when saved and user has wrap alignment true + // as preference setting + SwingUtilities.invokeLater(new Runnable() { - scrollX = av.startRes - av.endRes; - } - - if (scrollX != 0 || scrollY != 0) - { - idPanel.idCanvas.fastPaint(scrollY); - seqPanel.seqCanvas.fastPaint(scrollX, - scrollY); - scalePanel.repaint(); - - if (av.getShowAnnotation()) + @Override + public void run() { - annotationPanel.fastPaint(scrollX); + // When updating scrolling to use ViewportChange events, this code + // could not be validated and it is not clear if it is now being + // called. Log warning here in case it is called and unforeseen + // problems occur + Cache.log.warn( + "Unexpected path through code: Wrapped jar file opened with wrap alignment set in preferences"); + + // scroll to start of panel + ranges.setStartRes(0); + ranges.setStartSeq(0); } - } + }); } + repaint(); } - public void paintAlignment(boolean updateOverview) + /* (non-Javadoc) + * @see jalview.api.AlignmentViewPanel#paintAlignment(boolean) + */ + @Override + public void paintAlignment(boolean updateOverview, + boolean updateStructures) { + final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), + av.isShowAutocalculatedAbove()); + sorter.sort(getAlignment().getAlignmentAnnotation(), + av.getSortAnnotationsBy()); repaint(); - if(updateOverview) + if (updateStructures) + { + av.getStructureSelectionManager().sequenceColoursChanged(this); + } + if (updateOverview) { - jalview.structure.StructureSelectionManager.getStructureSelectionManager() - .sequenceColoursChanged(this); if (overviewPanel != null) { @@ -582,171 +863,207 @@ public class AlignmentPanel /** * DOCUMENT ME! - * - * @param g DOCUMENT ME! + * + * @param g + * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { - invalidate(); + invalidate(); // needed so that the id width adjuster works correctly - 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(); + validate(); // needed so that the id width adjuster works correctly - if (av.hasHiddenColumns) - { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; - } + /* + * set scroll bar positions - tried to remove but necessary for split panel to resize correctly + * though I still think this call should be elsewhere. + */ + ViewportRanges ranges = av.getRanges(); + setScrollValues(ranges.getStartRes(), ranges.getStartSeq()); + } - int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel. - seqCanvas.getWidth()); - if (canvasWidth > 0) - { - int max = maxwidth / - seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas. - getWidth()) + - 1; - vscroll.setMaximum(max); - vscroll.setUnitIncrement(1); - vscroll.setVisibleAmount(1); - } - } - else - { - setScrollValues(av.getStartRes(), av.getStartSeq()); - } + /** + * Set vertical scroll bar position, and number of increments, for wrapped + * panel + * + * @param topLeftColumn + * the column position at top left (0..) + */ + private void setScrollingForWrappedPanel(int topLeftColumn) + { + ViewportRanges ranges = av.getRanges(); + int scrollPosition = ranges.getWrappedScrollPosition(topLeftColumn); + int maxScroll = ranges.getWrappedMaxScroll(topLeftColumn); + + /* + * a scrollbar's value can be set to at most (maximum-extent) + * so we add extent (1) to the maxScroll value + */ + vscroll.setUnitIncrement(1); + vscroll.setValues(scrollPosition, 1, 0, maxScroll + 1); } /** * DOCUMENT ME! - * - * @param pg DOCUMENT ME! - * @param pf DOCUMENT ME! - * @param pi DOCUMENT ME! - * + * + * @param pg + * DOCUMENT ME! + * @param pf + * DOCUMENT ME! + * @param pi + * DOCUMENT ME! + * * @return DOCUMENT ME! - * - * @throws PrinterException DOCUMENT ME! + * + * @throws PrinterException + * DOCUMENT ME! */ + @Override public int print(Graphics pg, PageFormat pf, int pi) - throws PrinterException + throws PrinterException { - pg.translate( (int) pf.getImageableX(), (int) pf.getImageableY()); + pg.translate((int) pf.getImageableX(), (int) pf.getImageableY()); int pwidth = (int) pf.getImageableWidth(); int pheight = (int) pf.getImageableHeight(); if (av.getWrapAlignment()) { - return printWrappedAlignment(pg, pwidth, pheight, pi); + return printWrappedAlignment(pwidth, pheight, pi, pg); } else { - return printUnwrapped(pg, pwidth, pheight, pi); + return printUnwrapped(pwidth, pheight, pi, pg, pg); } } /** * DOCUMENT ME! - * - * @param pg DOCUMENT ME! - * @param pwidth DOCUMENT ME! - * @param pheight DOCUMENT ME! - * @param pi DOCUMENT ME! - * + * + * @param pg + * DOCUMENT ME! + * @param pwidth + * DOCUMENT ME! + * @param pheight + * DOCUMENT ME! + * @param pi + * DOCUMENT ME! + * * @return DOCUMENT ME! - * - * @throws PrinterException DOCUMENT ME! + * + * @throws PrinterException + * DOCUMENT ME! + */ + /** + * Draws the alignment image, including sequence ids, sequences, and + * annotation labels and annotations if shown, on either one or two Graphics + * context. + * + * @param pageWidth + * @param pageHeight + * @param pi + * @param idGraphics + * the graphics context for sequence ids and annotation labels + * @param alignmentGraphics + * the graphics context for sequences and annotations (may or may not + * be the same context as idGraphics) + * @return + * @throws PrinterException */ - public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) - throws PrinterException + public int printUnwrapped(int pageWidth, int pageHeight, int pi, + Graphics idGraphics, Graphics alignmentGraphics) + throws PrinterException { - int idWidth = getVisibleIdWidth(); - FontMetrics fm = getFontMetrics(av.getFont()); - int scaleHeight = av.charHeight + fm.getDescent(); - - pg.setColor(Color.white); - pg.fillRect(0, 0, pwidth, pheight); - pg.setFont(av.getFont()); + final int idWidth = getVisibleIdWidth(false); - //////////////////////////////////// - /// How many sequences and residues can we fit on a printable page? - int totalRes = (pwidth - idWidth) / av.getCharWidth(); + /* + * Get the horizontal offset to where we draw the sequences. + * This is idWidth if using a single Graphics context, else zero. + */ + final int alignmentGraphicsOffset = idGraphics != alignmentGraphics ? 0 + : idWidth; - int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) - - 1; + FontMetrics fm = getFontMetrics(av.getFont()); + int charHeight = av.getCharHeight(); + int scaleHeight = charHeight + fm.getDescent(); - int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1; + idGraphics.setColor(Color.white); + idGraphics.fillRect(0, 0, pageWidth, pageHeight); + idGraphics.setFont(av.getFont()); - ///////////////////////////// - /// Only print these sequences and residues on this page - int startRes; + /* + * How many sequences and residues can we fit on a printable page? + */ + int totalRes = (pageWidth - idWidth) / av.getCharWidth(); - ///////////////////////////// - /// Only print these sequences and residues on this page - int endRes; + int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; - ///////////////////////////// - /// Only print these sequences and residues on this page - int startSeq; + int alignmentWidth = av.getAlignment().getWidth(); + int pagesWide = (alignmentWidth / totalRes) + 1; - ///////////////////////////// - /// Only print these sequences and residues on this page - int endSeq; - startRes = (pi % pagesWide) * totalRes; - endRes = (startRes + totalRes) - 1; + final int startRes = (pi % pagesWide) * totalRes; + int endRes = (startRes + totalRes) - 1; - if (endRes > (av.getAlignment().getWidth() - 1)) + if (endRes > (alignmentWidth - 1)) { - endRes = av.getAlignment().getWidth() - 1; + endRes = alignmentWidth - 1; } - startSeq = (pi / pagesWide) * totalSeq; - endSeq = startSeq + totalSeq; + final int startSeq = (pi / pagesWide) * totalSeq; + int endSeq = startSeq + totalSeq; - if (endSeq > av.getAlignment().getHeight()) + int alignmentHeight = av.getAlignment().getHeight(); + if (endSeq > alignmentHeight) { - endSeq = av.getAlignment().getHeight(); + endSeq = alignmentHeight; } - int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight; + int pagesHigh = ((alignmentHeight / totalSeq) + 1) * pageHeight; - if (av.showAnnotation) + if (av.isShowAnnotation()) { - pagesHigh += annotationPanel.adjustPanelHeight() + 3; + pagesHigh += getAnnotationPanel().adjustPanelHeight() + 3; } - pagesHigh /= pheight; + pagesHigh /= pageHeight; if (pi >= (pagesWide * pagesHigh)) { return Printable.NO_SUCH_PAGE; } - - //draw Scale - pg.translate(idWidth, 0); - scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight); - pg.translate( -idWidth, scaleHeight); - - //////////////// - // Draw the ids + final int alignmentDrawnHeight = (endSeq - startSeq) * charHeight + 3; + + /* + * draw the Scale at horizontal offset, then reset to top left (0, 0) + */ + alignmentGraphics.translate(alignmentGraphicsOffset, 0); + getScalePanel().drawScale(alignmentGraphics, startRes, endRes, + pageWidth - idWidth, scaleHeight); + alignmentGraphics.translate(-alignmentGraphicsOffset, 0); + + /* + * Draw the sequence ids, offset for scale height, + * then reset to top left (0, 0) + */ + idGraphics.translate(0, scaleHeight); + idGraphics.setFont(getIdPanel().getIdCanvas().getIdfont()); Color currentColor = null; Color currentTextColor = null; - pg.setFont(idPanel.idCanvas.idfont); - SequenceI seq; for (int i = startSeq; i < endSeq; i++) { seq = av.getAlignment().getSequenceAt(i); - if ( (av.getSelectionGroup() != null) && - av.getSelectionGroup().getSequences(null).contains(seq)) + if ((av.getSelectionGroup() != null) + && av.getSelectionGroup().getSequences(null).contains(seq)) { + /* + * gray out ids of sequences in selection group (if any) + */ currentColor = Color.gray; currentTextColor = Color.black; } @@ -756,40 +1073,57 @@ public class AlignmentPanel currentTextColor = Color.black; } - pg.setColor(currentColor); - pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, - av.getCharHeight()); + idGraphics.setColor(currentColor); + idGraphics.fillRect(0, (i - startSeq) * charHeight, idWidth, + charHeight); - pg.setColor(currentTextColor); + idGraphics.setColor(currentTextColor); int xPos = 0; - if (av.rightAlignIds) + String displayId = seq.getDisplayId(av.getShowJVSuffix()); + if (av.isRightAlignIds()) { - fm = pg.getFontMetrics(); - xPos = idWidth - fm.stringWidth( - seq.getDisplayId(av.getShowJVSuffix()) - ) - 4; + fm = idGraphics.getFontMetrics(); + xPos = idWidth - fm.stringWidth(displayId) - 4; } - pg.drawString(seq.getDisplayId(av.getShowJVSuffix()), - xPos, - ( ( (i - startSeq) * av.charHeight) + av.getCharHeight()) - - (av.getCharHeight() / 5)); + idGraphics.drawString(displayId, xPos, + (((i - startSeq) * charHeight) + charHeight) + - (charHeight / 5)); } - - pg.setFont(av.getFont()); - - // draw main sequence panel - pg.translate(idWidth, 0); - seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0); - - if (av.showAnnotation && (endSeq == av.alignment.getHeight())) + idGraphics.setFont(av.getFont()); + idGraphics.translate(0, -scaleHeight); + + /* + * draw the sequences, offset for scale height, and id width (if using a + * single graphics context), then reset to (0, scale height) + */ + alignmentGraphics.translate(alignmentGraphicsOffset, scaleHeight); + getSeqPanel().seqCanvas.drawPanelForPrinting(alignmentGraphics, startRes, + endRes, startSeq, endSeq); + alignmentGraphics.translate(-alignmentGraphicsOffset, 0); + + if (av.isShowAnnotation() && (endSeq == alignmentHeight)) { - pg.translate( -idWidth - 3, (endSeq - startSeq) * av.charHeight + 3); - alabels.drawComponent( (Graphics2D) pg, idWidth); - pg.translate(idWidth + 3, 0); - annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes + - 1); + /* + * draw annotation labels; drawComponent() translates by + * getScrollOffset(), so compensate for that first; + * then reset to (0, scale height) + */ + int offset = getAlabels().getScrollOffset(); + idGraphics.translate(0, -offset); + idGraphics.translate(0, alignmentDrawnHeight); + getAlabels().drawComponent(idGraphics, idWidth); + idGraphics.translate(0, -alignmentDrawnHeight); + + /* + * draw the annotations starting at + * (idOffset, alignmentHeight) from (0, scaleHeight) + */ + alignmentGraphics.translate(alignmentGraphicsOffset, + alignmentDrawnHeight); + getAnnotationPanel().renderer.drawComponent(getAnnotationPanel(), av, + alignmentGraphics, -1, startRes, endRes + 1); } return Printable.PAGE_EXISTS; @@ -797,49 +1131,52 @@ public class AlignmentPanel /** * DOCUMENT ME! - * - * @param pg DOCUMENT ME! - * @param pwidth DOCUMENT ME! - * @param pheight DOCUMENT ME! - * @param pi DOCUMENT ME! - * + * + * @param pg + * DOCUMENT ME! + * @param pwidth + * DOCUMENT ME! + * @param pheight + * DOCUMENT ME! + * @param pi + * DOCUMENT ME! + * * @return DOCUMENT ME! - * - * @throws PrinterException DOCUMENT ME! + * + * @throws PrinterException + * DOCUMENT ME! */ - public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, - int pi) - throws PrinterException + public int printWrappedAlignment(int pwidth, int pheight, int pi, + Graphics pg) 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 - + annotationHeight; + 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; + maxwidth = av.getAlignment().getHiddenColumns() + .absoluteToVisibleColumn(maxwidth) - 1; } - int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - - idWidth); + int resWidth = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(pwidth - idWidth); int totalHeight = cHeight * (maxwidth / resWidth + 1); @@ -847,7 +1184,7 @@ public class AlignmentPanel pg.fillRect(0, 0, pwidth, pheight); pg.setFont(av.getFont()); - //////////////// + // ////////////// // Draw the ids pg.setColor(Color.black); @@ -859,43 +1196,41 @@ public class AlignmentPanel 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; - } - while (ypos < totalHeight); + } while (ypos < totalHeight); pg.translate(idWidth, 0); - seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0); + getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(pg, pwidth - idWidth, + totalHeight, 0); - if ( (pi * pheight) < totalHeight) + if ((pi * pheight) < totalHeight) { return Printable.PAGE_EXISTS; @@ -906,305 +1241,606 @@ public class AlignmentPanel } } - 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) + { + int w = getIdPanel().getWidth(); + return (w > 0 ? w : calculateIdWidth().width + 4); + } + return idwidth.intValue() + 4; + } - int height = ( (av.alignment.getHeight() + 1) * av.charHeight) - + scalePanel.getHeight(); - int width = getVisibleIdWidth() + (maxwidth * av.charWidth); + /** + * Builds an image of the alignment of the specified type (EPS/PNG/SVG) and + * writes it to the specified file + * + * @param type + * @param file + */ + void makeAlignmentImage(ImageMaker.TYPE type, File file) + { + final int borderBottomOffset = 5; - if (av.getWrapAlignment()) + AlignmentDimension aDimension = getAlignmentDimension(); + // todo use a lambda function in place of callback here? + ImageWriterI writer = new ImageWriterI() { - 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 + @Override + public void exportImage(Graphics graphics) throws Exception { - width = seqPanel.getWidth() + getVisibleIdWidth(); + if (av.getWrapAlignment()) + { + printWrappedAlignment(aDimension.getWidth(), + aDimension.getHeight() + borderBottomOffset, 0, graphics); + } + else + { + printUnwrapped(aDimension.getWidth(), aDimension.getHeight(), 0, + graphics, graphics); + } } + }; + + String fileTitle = alignFrame.getTitle(); + ImageExporter exporter = new ImageExporter(writer, alignFrame, type, + fileTitle); + int imageWidth = aDimension.getWidth(); + int imageHeight = aDimension.getHeight() + borderBottomOffset; + String of = MessageManager.getString("label.alignment"); + exporter.doExport(file, this, imageWidth, imageHeight, of); + } - } - else if (av.getShowAnnotation()) + /** + * Calculates and returns a suitable width and height (in pixels) for an + * exported image + * + * @return + */ + public AlignmentDimension getAlignmentDimension() + { + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { - height += annotationPanel.adjustPanelHeight() + 3; + maxwidth = av.getAlignment().getHiddenColumns() + .absoluteToVisibleColumn(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 (Jalview.isHeadlessMode()) { - 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) + else if (av.isShowAnnotation()) { - System.out.println("########################\n" - + "OUT OF MEMORY " + file + "\n" - + "########################"); - - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of Memory Creating Image!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - JOptionPane.WARNING_MESSAGE); - System.out.println("Create IMAGE: " + err); - System.gc(); - + height += getAnnotationPanel().adjustPanelHeight() + 3; } - catch (Exception ex) - { - ex.printStackTrace(); - } - } + return new AlignmentDimension(width, height); - /** - * DOCUMENT ME! - */ - public void makeEPS(File epsFile) - { - makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile); - } - - /** - * DOCUMENT ME! - */ - public void makePNG(File pngFile) - { - makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile); } public void makePNGImageMap(File imgMapFile, String imageName) { - ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS - ////////////////////////////////////////////// - int idWidth = getVisibleIdWidth(); + // /////ONLY WORKS WITH NON WRAPPED ALIGNMENTS + // //////////////////////////////////////////// + int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); - int scaleHeight = av.charHeight + fm.getDescent(); + int scaleHeight = av.getCharHeight() + fm.getDescent(); // Gen image map - ////////////////////////////////// + // //////////////////////////////// if (imgMapFile != null) { try { - int s, sSize = av.alignment.getHeight(), - res, alwidth = av.alignment.getWidth(), g, gSize, f, fSize, sy; - StringBuffer text = new StringBuffer(); + int sSize = av.getAlignment().getHeight(); + int alwidth = av.getAlignment().getWidth(); PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); - out.println(jalview.io.HTMLOutput.getImageMapHTML()); - out.println("" - + ""); + out.println(HTMLOutput.getImageMapHTML()); + out.println("" + + ""); - for (s = 0; s < sSize; s++) + for (int s = 0; s < sSize; s++) { - sy = s * av.charHeight + scaleHeight; + int sy = s * av.getCharHeight() + scaleHeight; - SequenceI seq = av.alignment.getSequenceAt(s); - SequenceFeature[] features = seq.getDatasetSequence(). - getSequenceFeatures(); - SequenceGroup[] groups = av.alignment.findAllGroups(seq); - for (res = 0; res < alwidth; res++) + SequenceI seq = av.getAlignment().getSequenceAt(s); + SequenceGroup[] groups = av.getAlignment().findAllGroups(seq); + for (int column = 0; column < alwidth; column++) { - text = new StringBuffer(); - Object obj = null; - if (av.alignment.isNucleotide()) + StringBuilder text = new StringBuilder(512); + String triplet = null; + if (av.getAlignment().isNucleotide()) { - obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) + - ""); + triplet = ResidueProperties.nucleotideName.get(seq + .getCharAt(column) + ""); } else { - obj = ResidueProperties.aa2Triplet.get( - seq.getCharAt(res) + ""); + triplet = ResidueProperties.aa2Triplet.get(seq.getCharAt(column) + + ""); } - 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++) + int seqPos = seq.findPosition(column); + int gSize = groups.length; + for (int g = 0; g < gSize; g++) { if (text.length() < 1) { - text.append(" res) + if (groups[g].getStartRes() < column + && groups[g].getEndRes() > column) { - text.append("
" + groups[g].getName() + ""); + text.append("
").append(groups[g].getName()) + .append(""); } } - if (features != null) + if (text.length() < 1) { - if (text.length() < 1) - { - text.append(" features = seq.findFeatures(column, column); + for (SequenceFeature sf : features) { - - if ( (features[f].getBegin() <= seq.findPosition(res)) && - (features[f].getEnd() >= seq.findPosition(res))) + if (sf.isContactFeature()) { - if (features[f].getType().equals("disulfide bond")) - { - if (features[f].getBegin() == seq.findPosition(res) - || features[f].getEnd() == seq.findPosition(res)) - { - text.append("
disulfide bond " + features[f].getBegin() + - ":" + - features[f].getEnd()); - } - } - else + text.append("
").append(sf.getType()).append(" ") + .append(sf.getBegin()).append(":") + .append(sf.getEnd()); + } + else + { + text.append("
"); + text.append(sf.getType()); + String description = sf.getDescription(); + if (description != null + && !sf.getType().equals(description)) { - text.append("
"); - text.append(features[f].getType()); - if (features[f].getDescription() != null && - !features[f]. - getType().equals(features[f].getDescription())) - { - text.append(" " + features[f].getDescription()); - } - - if (features[f].getValue("status") != null) - { - text.append(" (" + features[f].getValue("status") + ")"); - } + description = description.replace("\"", """); + text.append(" ").append(description); } } - + String status = sf.getStatus(); + if (status != null && !"".equals(status)) + { + text.append(" (").append(status).append(")"); + } + } + if (text.length() > 1) + { + text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">"); + out.println(text.toString()); } - } - if (text.length() > 1) - { - text.append("')\"; onMouseOut=\"toolTip()\"; href=\"#\">"); - out.println(text.toString()); } } } out.println(""); out.close(); - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } - } ///////////END OF IMAGE MAP + } // /////////END OF IMAGE MAP } 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")) + && System.getProperty("java.awt.headless").equals("true")) { - seqPanelWidth = alignFrame.getWidth() - - getVisibleIdWidth() - - vscroll.getPreferredSize().width - - alignFrame.getInsets().left - - alignFrame.getInsets().right; + seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth() + - vscroll.getPreferredSize().width + - alignFrame.getInsets().left - alignFrame.getInsets().right; } - int chunkWidth = seqPanel.seqCanvas.getWrappedCanvasWidth( - seqPanelWidth - ); + int chunkWidth = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(seqPanelWidth); - int hgap = av.charHeight; - if (av.scaleAboveWrapped) + int hgap = av.getCharHeight(); + if (av.getScaleAboveWrapped()) { - hgap += av.charHeight; + hgap += av.getCharHeight(); } 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 cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap + + annotationHeight; - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; + maxwidth = av.getAlignment().getHiddenColumns() + .absoluteToVisibleColumn(maxwidth) - 1; } - int height = ( (maxwidth / chunkWidth) + 1) * cHeight; + int height = ((maxwidth / chunkWidth) + 1) * cHeight; return height; } + + /** + * close the panel - deregisters all listeners and nulls any references to + * alignment data. + */ + public void closePanel() + { + PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas); + PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas()); + PaintRefresher.RemoveComponent(this); + + closeChildFrames(); + + /* + * try to ensure references are nulled + */ + if (annotationPanel != null) + { + annotationPanel.dispose(); + annotationPanel = null; + } + + if (av != null) + { + av.removePropertyChangeListener(propertyChangeListener); + propertyChangeListener = null; + StructureSelectionManager ssm = av.getStructureSelectionManager(); + ssm.removeStructureViewerListener(getSeqPanel(), null); + ssm.removeSelectionListener(getSeqPanel()); + ssm.removeCommandListener(av); + ssm.removeStructureViewerListener(getSeqPanel(), null); + ssm.removeSelectionListener(getSeqPanel()); + av.dispose(); + av = null; + } + else + { + if (Cache.log.isDebugEnabled()) + { + Cache.log.warn("Closing alignment panel which is already closed."); + } + } + } + + /** + * Close any open dialogs that would be orphaned when this one is closed + */ + protected void closeChildFrames() + { + if (overviewPanel != null) + { + overviewPanel.dispose(); + overviewPanel = null; + } + if (calculationDialog != null) + { + calculationDialog.closeFrame(); + calculationDialog = null; + } + } + + /** + * hides or shows dynamic annotation rows based on groups and av state flags + */ + public void updateAnnotation() + { + updateAnnotation(false, false); + } + + public void updateAnnotation(boolean applyGlobalSettings) + { + updateAnnotation(applyGlobalSettings, false); + } + + public void updateAnnotation(boolean applyGlobalSettings, + boolean preserveNewGroupSettings) + { + av.updateGroupAnnotationSettings(applyGlobalSettings, + preserveNewGroupSettings); + adjustAnnotationHeight(); + } + + @Override + public AlignmentI getAlignment() + { + return av == null ? null : av.getAlignment(); + } + + @Override + public String getViewName() + { + return av.viewName; + } + + /** + * Make/Unmake this alignment panel the current input focus + * + * @param b + */ + public void setSelected(boolean b) + { + try + { + if (alignFrame.getSplitViewContainer() != null) + { + /* + * bring enclosing SplitFrame to front first if there is one + */ + ((SplitFrame) alignFrame.getSplitViewContainer()).setSelected(b); + } + alignFrame.setSelected(b); + } catch (Exception ex) + { + } + + if (b) + { + alignFrame.setDisplayedView(this); + } + } + + @Override + public StructureSelectionManager getStructureSelectionManager() + { + return av.getStructureSelectionManager(); + } + + @Override + public void raiseOOMWarning(String string, OutOfMemoryError error) + { + new OOMWarning(string, error, this); + } + + @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; + } + + /** + * Follow a scrolling change in the (cDNA/Protein) complementary alignment. + * The aim is to keep the two alignments 'lined up' on their centre columns. + * + * @param sr + * holds mapped region(s) of this alignment that we are scrolling + * 'to'; may be modified for sequence offset by this method + * @param verticalOffset + * the number of visible sequences to show above the mapped region + */ + protected void scrollToCentre(SearchResultsI sr, int verticalOffset) + { + scrollToPosition(sr, verticalOffset, true, true); + } + + /** + * Set a flag to say do not scroll any (cDNA/protein) complement. + * + * @param b + */ + protected void setToScrollComplementPanel(boolean b) + { + this.scrollComplementaryPanel = b; + } + + /** + * Get whether to scroll complement panel + * + * @return true if cDNA/protein complement panels should be scrolled + */ + protected boolean isSetToScrollComplementPanel() + { + return this.scrollComplementaryPanel; + } + + /** + * Redraw sensibly. + * + * @adjustHeight if true, try to recalculate panel height for visible + * annotations + */ + protected void refresh(boolean adjustHeight) + { + validateAnnotationDimensions(adjustHeight); + addNotify(); + if (adjustHeight) + { + // sort, repaint, update overview + paintAlignment(true, false); + } + else + { + // lightweight repaint + repaint(); + } + } + + @Override + /** + * Property change event fired when a change is made to the viewport ranges + * object associated with this alignment panel's viewport + */ + public void propertyChange(PropertyChangeEvent evt) + { + // update this panel's scroll values based on the new viewport ranges values + ViewportRanges ranges = av.getRanges(); + int x = ranges.getStartRes(); + int y = ranges.getStartSeq(); + setScrollValues(x, y); + + // now update any complementary alignment (its viewport ranges object + // is different so does not get automatically updated) + if (isSetToScrollComplementPanel()) + { + setToScrollComplementPanel(false); + av.scrollComplementaryAlignment(); + setToScrollComplementPanel(true); + } + } + + /** + * Set the reference to the PCA/Tree chooser dialog for this panel. This + * reference should be nulled when the dialog is closed. + * + * @param calculationChooser + */ + public void setCalculationDialog(CalculationChooser calculationChooser) + { + calculationDialog = calculationChooser; + } + + /** + * Returns the reference to the PCA/Tree chooser dialog for this panel (null + * if none is open) + */ + public CalculationChooser getCalculationDialog() + { + return calculationDialog; + } }