X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=8619ad0d7deb8abfb3284dcb2c38b96547181739;hb=801c367379086cc38bf4d3059a8e30ca9f4e78c0;hp=170eacfaf671e6d03b690c7465465e18ad90a6c4;hpb=e015538903c8cabb2b90dd030e3e0c419a730db9;p=jalview.git diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 170eacf..c43e0b6 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,114 +1,196 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) - * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.gui; -import java.beans.*; -import java.io.*; -import java.util.Hashtable; -import java.util.Vector; - -import java.awt.*; -import java.awt.event.*; -import java.awt.print.*; -import javax.swing.*; - +import jalview.analysis.AnnotationSorter; +import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; +import jalview.api.SequenceRenderer; import jalview.bin.Cache; -import jalview.datamodel.*; -import jalview.jbgui.*; -import jalview.schemes.*; +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.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.Graphics2D; +import java.awt.event.AdjustmentEvent; +import java.awt.event.AdjustmentListener; +import java.awt.event.ComponentAdapter; +import java.awt.event.ComponentEvent; +import java.awt.image.BufferedImage; +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; /** - * DOCUMENT ME! + * The main panel of an AlignFrame, containing holders for the IdPanel, + * SeqPanel, AnnotationLabels (a JPanel), and AnnotationPanel. + * + * Additional holders contain an IdPanelWidthAdjuster space above the idPanel, + * AnnotationScroller (JScrollPane for AnnotationPanel), and vertical and + * horizontal scrollbars. + * + * * * @author $author$ * @version $Revision: 1.161 $ */ +@SuppressWarnings("serial") public class AlignmentPanel extends GAlignmentPanel implements - AdjustmentListener, Printable, AlignmentViewPanel + AdjustmentListener, Printable, AlignmentViewPanel, ViewportListenerI { public AlignViewport av; OverviewPanel overviewPanel; - SeqPanel seqPanel; + private SeqPanel seqPanel; - IdPanel idPanel; + private IdPanel idPanel; IdwidthAdjuster idwidthAdjuster; - /** DOCUMENT ME!! */ public AlignFrame alignFrame; - ScalePanel scalePanel; + private ScalePanel scalePanel; + + private AnnotationPanel annotationPanel; + + private AnnotationLabels alabels; - AnnotationPanel annotationPanel; + private int hextent = 0; - AnnotationLabels alabels; + private int vextent = 0; - // this value is set false when selection area being dragged - boolean fastPaint = true; + /* + * Flag set while scrolling to follow complementary cDNA/protein scroll. When + * false, suppresses invoking the same method recursively. + */ + private boolean scrollComplementaryPanel = true; - int hextent = 0; + private PropertyChangeListener propertyChangeListener; - int vextent = 0; + private CalculationChooser calculationDialog; /** * Creates a new AlignmentPanel object. * * @param af - * DOCUMENT ME! * @param av - * DOCUMENT ME! */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { + setBackground(Color.white); // BH 2019 + setOpaque(true); 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); - - annotationScroller.setViewportView(annotationPanel); - annotationSpaceFillerHolder.add(alabels, BorderLayout.CENTER); + setAnnotationPanel(new AnnotationPanel(this)); + setAlabels(new AnnotationLabels(this)); - scalePanelHolder.add(scalePanel, BorderLayout.CENTER); - seqPanelHolder.add(seqPanel, BorderLayout.CENTER); + annotationScroller.setViewportView(getAnnotationPanel()); + annotationSpaceFillerHolder.add(getAlabels(), BorderLayout.CENTER); + if (!av.isShowAnnotation()) + { + annotationScroller.setVisible(false); + annotationSpaceFillerHolder.setVisible(false); + } + 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); + ViewportRanges.sTest += "AP.resize chht=" + av.getCharHeight() + + "canvHt=" + getSeqPanel().seqCanvas.getHeight() + " " + + heightInSeq + "\n"; + } + } + + }); + final AlignmentPanel ap = this; - av.addPropertyChangeListener(new PropertyChangeListener() + propertyChangeListener = new PropertyChangeListener() { + @Override public void propertyChange(PropertyChangeEvent evt) { if (evt.getPropertyName().equals("alignment")) @@ -117,19 +199,34 @@ public class AlignmentPanel extends GAlignmentPanel implements 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); } @@ -142,25 +239,22 @@ public class AlignmentPanel extends GAlignmentPanel implements // to prevent drawing old image FontMetrics fm = getFontMetrics(av.getFont()); - scalePanelHolder.setPreferredSize(new Dimension(10, av.charHeight - + fm.getDescent())); - idSpaceFillerPanel1.setPreferredSize(new Dimension(10, av.charHeight - + 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(); + // BH 2018 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(); } @@ -174,16 +268,29 @@ public class AlignmentPanel extends GAlignmentPanel implements public Dimension calculateIdWidth() { // calculate sensible default width when no preference is available - - int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); - int maxwidth = Math.max(20, - Math.min(afwidth - 200, (int) 2 * afwidth / 3)); - return calculateIdWidth(maxwidth); + 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 + * + * @param maxwidth + * -1 or maximum width allowed for IdWidth * @return Dimension giving the maximum width of the alignment label panel * that should be used. */ @@ -191,8 +298,8 @@ public class AlignmentPanel extends GAlignmentPanel implements { Container c = new Container(); - FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(), - Font.ITALIC, av.font.getSize())); + FontMetrics fm = c.getFontMetrics( + new Font(av.font.getName(), Font.ITALIC, av.font.getSize())); AlignmentI al = av.getAlignment(); int i = 0; @@ -218,7 +325,7 @@ 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) { @@ -233,129 +340,159 @@ public class AlignmentPanel extends GAlignmentPanel implements } } - return new Dimension(maxwidth<0 ? idWidth : Math.min(maxwidth, idWidth), 12); + return new Dimension( + maxwidth < 0 ? idWidth : Math.min(maxwidth, idWidth), 12); } /** - * Highlight the given results on the alignment. + * Highlight the given results on the alignment * */ - public void highlightSearchResults(SearchResults results) + public void highlightSearchResults(SearchResultsI results) { - scrollToPosition(results); - seqPanel.seqCanvas.highlightSearchResults(results); + boolean scrolled = scrollToPosition(results, 0, 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) and redraw the overview + * Scroll the view to show the position of the highlighted region in results + * (if any) * - * @param results + * @param searchResults + * @return */ - public boolean scrollToPosition(SearchResults results) + public boolean scrollToPosition(SearchResultsI searchResults) { - return scrollToPosition(results, true); + return scrollToPosition(searchResults, 0, false); } /** - * scroll the view to show the position of the highlighted region in results - * (if any) + * 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 redrawOverview - * - when set, the overview will be recalculated (takes longer) - * @return false if results were not found + * @param verticalOffset + * if greater than zero, allows scrolling to a position below the + * first displayed sequence + * @param centre + * if true, try to centre the search results horizontally in the view + * @return */ - public boolean scrollToPosition(SearchResults results, - boolean redrawOverview) - { - int startv, endv, starts, ends, width; - // 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.getAlignment() != null) - { - 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) - { - return false; - } - int start = r[0]; - int end = r[1]; - // System.err.println("Seq : "+seqIndex+" Scroll to "+start+","+end); // - // DEBUG - if (start < 0) + protected boolean scrollToPosition(SearchResultsI results, + int verticalOffset, 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) + { + 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.hasHiddenColumns()) + { + HiddenColumns hidden = av.getAlignment().getHiddenColumns(); + start = hidden.absoluteToVisibleColumn(start); + end = hidden.absoluteToVisibleColumn(end); + if (start == end) { - return false; + if (!hidden.isVisible(r[0])) + { + // don't scroll - position isn't visible + return false; + } } - if (end == seq.getEnd()) + } + + /* + * allow for offset of target sequence (actually scroll to one above it) + */ + seqIndex = Math.max(0, seqIndex - verticalOffset); + boolean scrollNeeded = true; + + if (!av.getWrapAlignment()) + { + if ((startv = ranges.getStartRes()) >= start) { - return false; + /* + * Scroll left to make start of search results visible + */ + setScrollValues(start, seqIndex); } - if (av.hasHiddenColumns()) + else if ((endv = ranges.getEndRes()) <= end) { - start = av.getColumnSelection().findColumnPosition(start); - end = av.getColumnSelection().findColumnPosition(end); - if (start==end) - { - if (!av.getColumnSelection().isVisible(r[0])) - { - // don't scroll - position isn't visible - return false; - } - } + /* + * Scroll right to make end of search results visible + */ + setScrollValues(startv + end - endv, seqIndex); } - if (!av.wrapAlignment) + else if ((starts = ranges.getStartSeq()) > seqIndex) { - if ((startv = av.getStartRes()) >= start) - { - setScrollValues(start - 1, seqIndex); - } - else if ((endv = av.getEndRes()) <= end) - { - setScrollValues(startv + 1 + end - endv, seqIndex); - } - else if ((starts = av.getStartSeq()) > seqIndex) - { - setScrollValues(av.getStartRes(), seqIndex); - } - else if ((ends = av.getEndSeq()) <= seqIndex) - { - setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); - } + /* + * Scroll up to make start of search results visible + */ + setScrollValues(ranges.getStartRes(), seqIndex); } - else + else if ((ends = ranges.getEndSeq()) <= seqIndex) { - scrollToWrappedVisible(start); + /* + * 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; } - if (redrawOverview && overviewPanel != null) + else { - overviewPanel.setBoxPosition(); + scrollNeeded = ranges.scrollToWrappedVisible(start); } - paintAlignment(redrawOverview); - return true; - } - void scrollToWrappedVisible(int res) - { - int cwidth = seqPanel.seqCanvas - .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); - if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth)) - { - vscroll.setValue((res / cwidth)); - av.startRes = vscroll.getValue() * cwidth; - } + paintAlignment(false, false); + return scrollNeeded; } /** @@ -381,12 +518,13 @@ public class AlignmentPanel extends GAlignmentPanel implements /** * - * @param b Hide or show annotation panel - * + * @param b + * Hide or show annotation panel + * */ public void setAnnotationVisible(boolean b) { - if (!av.wrapAlignment) + if (!av.getWrapAlignment()) { annotationSpaceFillerHolder.setVisible(b); annotationScroller.setVisible(b); @@ -395,9 +533,10 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** - * automatically adjust annotation panel height for new annotation - * whilst ensuring the alignment is still visible. + * automatically adjust annotation panel height for new annotation whilst + * ensuring the alignment is still visible. */ + @Override public void adjustAnnotationHeight() { // TODO: display vertical annotation scrollbar if necessary @@ -408,48 +547,57 @@ public class AlignmentPanel extends GAlignmentPanel implements } validateAnnotationDimensions(true); addNotify(); - paintAlignment(true); + // TODO: many places call this method and also paintAlignment with various + // different settings. this means multiple redraws are triggered... + paintAlignment(true, av.needToUpdateStructureViews()); } + /** * calculate the annotation dimensions and refresh slider values accordingly. - * need to do repaints/notifys afterwards. + * need to do repaints/notifys afterwards. */ - protected void validateAnnotationDimensions(boolean adjustPanelHeight) { - int height = annotationPanel.adjustPanelHeight(); - - if (hscroll.isVisible()) - { - height += hscroll.getPreferredSize().height; - } - if (height > alignFrame.getHeight() / 2) - { - height = alignFrame.getHeight() / 2; - } - if (!adjustPanelHeight) - { - // maintain same window layout whilst updating sliders - height=annotationScroller.getSize().height; - } + protected void validateAnnotationDimensions(boolean adjustPanelHeight) + { + // BH 2018.04.18 comment: addNotify() is not appropriate here. We + // are not changing ancestors, and keyboard action listeners do + // not need to be reset. addNotify() is a very expensive operation, + // requiring a full re-layout of all parents and children. + // Note in JComponent: + // This method is called by the toolkit internally and should + // not be called directly by programs. + // I note that addNotify() is called in several areas of Jalview. + + int annotationHeight = getAnnotationPanel().adjustPanelHeight(); + annotationHeight = getAnnotationPanel() + .adjustForAlignFrame(adjustPanelHeight, annotationHeight); + hscroll.addNotify(); - - annotationScroller.setPreferredSize(new Dimension(annotationScroller - .getWidth(), height)); + annotationScroller.setPreferredSize( + 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(); + annotationSpaceFillerHolder.getWidth(), annotationHeight)); + annotationScroller.validate(); annotationScroller.addNotify(); } /** - * DOCUMENT ME! + * update alignment layout for viewport settings * * @param wrap * DOCUMENT ME! */ - public void setWrapAlignment(boolean wrap) + public void updateLayout() { - av.startSeq = 0; + fontChanged(); // fires repaint + setAnnotationVisible(av.isShowAnnotation()); + boolean wrap = av.getWrapAlignment(); + ViewportRanges ranges = av.getRanges(); + ranges.setStartSeq(0); scalePanelHolder.setVisible(!wrap); hscroll.setVisible(!wrap); idwidthAdjuster.setVisible(!wrap); @@ -459,245 +607,248 @@ 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); + validateAnnotationDimensions(false); } - idSpaceFillerPanel1.setVisible(!wrap); - - repaint(); - } - - // return value is true if the scroll is valid - public boolean scrollUp(boolean up) - { - if (up) - { - if (vscroll.getValue() < 1) + int canvasWidth = getSeqPanel().seqCanvas.getWidth(); + if (canvasWidth > 0) + { // may not yet be laid out + if (wrap) { - return false; + int widthInRes = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(canvasWidth); + ranges.setViewportWidth(widthInRes); } - - fastPaint = false; - vscroll.setValue(vscroll.getValue() - 1); - } - else - { - if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight()) + else { - return false; - } + int widthInRes = (canvasWidth / av.getCharWidth()); + int heightInSeq = (getSeqPanel().seqCanvas.getHeight() + / av.getCharHeight()); - fastPaint = false; - vscroll.setValue(vscroll.getValue() + 1); + ranges.setViewportWidth(widthInRes); + ranges.setViewportHeight(heightInSeq); + } } - fastPaint = true; + idSpaceFillerPanel1.setVisible(!wrap); - return true; + repaint(); } /** - * DOCUMENT ME! + * Adjust row/column scrollers to show a visible position in the alignment. * - * @param right - * DOCUMENT ME! + * @param x + * visible column to scroll to + * @param y + * visible row to scroll to * - * @return DOCUMENT ME! */ - public boolean scrollRight(boolean right) + public void setScrollValues(int xpos, int ypos) { - if (!right) + int x = xpos; + int y = ypos; + + if (av == null || av.getAlignment() == null) { - if (hscroll.getValue() < 1) - { - return false; - } + return; + } - fastPaint = false; - hscroll.setValue(hscroll.getValue() - 1); + if (av.getWrapAlignment()) + { + setScrollingForWrappedPanel(x); } else { - if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth()) + int width = av.getAlignment().getVisibleWidth(); + int height = av.getAlignment().getHeight(); + + hextent = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); + vextent = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); + + if (hextent > width) { - return false; + hextent = width; } - fastPaint = false; - hscroll.setValue(hscroll.getValue() + 1); - } + if (vextent > height) + { + vextent = height; + } + + if ((hextent + x) > width) + { + x = width - hextent; + } + + if ((vextent + y) > height) + { + y = height - vextent; + } - fastPaint = true; + if (y < 0) + { + y = 0; + } - return true; + if (x < 0) + { + x = 0; + } + + // update the scroll values + hscroll.setValues(x, hextent, 0, width); + vscroll.setValues(y, vextent, 0, height); + } } /** - * Adjust row/column scrollers to show a visible position in the alignment. + * Respond to adjustment event when horizontal or vertical scrollbar is + * changed * - * @param x visible column to scroll to - * DOCUMENT ME! - * @param y visible row to scroll to - * + * @param evt + * adjustment event encoding whether hscroll or vscroll changed */ - public void setScrollValues(int x, int y) + @Override + public void adjustmentValueChanged(AdjustmentEvent evt) { - // System.err.println("Scroll to "+x+","+y); - if (av == null || av.getAlignment() == null) + if (av.getWrapAlignment()) { + adjustScrollingWrapped(evt); return; } - int width = av.getAlignment().getWidth(); - int height = av.getAlignment().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; + ViewportRanges ranges = av.getRanges(); - if (hextent > width) + if (evt.getSource() == hscroll) { - hextent = width; - } + int oldX = ranges.getStartRes(); + int oldwidth = ranges.getViewportWidth(); + int x = hscroll.getValue(); + int width = getSeqPanel().seqCanvas.getWidth() / av.getCharWidth(); - if (vextent > height) - { - vextent = height; + // 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 ((hextent + x) > width) + else if (evt.getSource() == vscroll) { - x = width - hextent; - } + int oldY = ranges.getStartSeq(); + int oldheight = ranges.getViewportHeight(); + int y = vscroll.getValue(); + int height = getSeqPanel().seqCanvas.getHeight() / av.getCharHeight(); - if ((vextent + y) > height) - { - y = height - vextent; - } - 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 ((y == oldY) && (height == oldheight)) + { + return; + } - if (x < 0) - { - x = 0; - } + ViewportRanges.sTest += "AP.valChanged chht=" + av.getCharHeight() + + "canvHt=" + getSeqPanel().seqCanvas.getHeight() + " " + + height + "\n"; - hscroll.setValues(x, hextent, 0, width); - vscroll.setValues(y, vextent, 0, height); + ranges.setViewportStartAndHeight(y, height); + } + repaint(); } /** - * DOCUMENT ME! + * Responds to a scroll change by setting the start position of the viewport. + * Does * * @param evt - * DOCUMENT ME! */ - 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(); + int newY = vscroll.getValue(); - if (av.getWrapAlignment()) + /* + * 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 + Jalview.execRunnable(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) + { if (overviewPanel != null) { overviewPanel.updateOverviewImage(); @@ -711,41 +862,46 @@ public class AlignmentPanel extends GAlignmentPanel implements * @param g * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { - invalidate(); - Dimension d = idPanel.idCanvas.getPreferredSize(); + invalidate(); // needed so that the id width adjuster works correctly + + Dimension d = getIdPanel().getIdCanvas().getPreferredSize(); idPanelHolder.setPreferredSize(d); hscrollFillerPanel.setPreferredSize(new Dimension(d.width, 12)); - validate(); - if (av.getWrapAlignment()) - { - int maxwidth = av.getAlignment().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()); + super.paintComponent(g); + } - 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); } /** @@ -763,6 +919,7 @@ public class AlignmentPanel extends GAlignmentPanel implements * @throws PrinterException * DOCUMENT ME! */ + @Override public int print(Graphics pg, PageFormat pf, int pi) throws PrinterException { @@ -773,408 +930,352 @@ public class AlignmentPanel extends GAlignmentPanel implements 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! - * - * @return DOCUMENT ME! + * Draws the alignment image, including sequence ids, sequences, and + * annotation labels and annotations if shown, on either one or two Graphics + * contexts. * + * @param pageWidth + * in pixels + * @param pageHeight + * in pixels + * @param pageIndex + * (0, 1, ...) + * @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 - * DOCUMENT ME! */ - public int printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) + public int printUnwrapped(int pageWidth, int pageHeight, int pageIndex, + Graphics idGraphics, Graphics alignmentGraphics) throws PrinterException { - int idWidth = getVisibleIdWidth(false); - 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()); - - // ////////////////////////////////// - // / How many sequences and residues can we fit on a printable page? - int totalRes = (pwidth - idWidth) / av.getCharWidth(); + final int idWidth = getVisibleIdWidth(false); - int totalSeq = (int) ((pheight - scaleHeight) / av.getCharHeight()) - 1; + /* + * 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 pagesWide = (av.getAlignment().getWidth() / totalRes) + 1; - - // /////////////////////////// - // / Only print these sequences and residues on this page - int startRes; + FontMetrics fm = getFontMetrics(av.getFont()); + final int charHeight = av.getCharHeight(); + final int scaleHeight = charHeight + fm.getDescent(); - // /////////////////////////// - // / Only print these sequences and residues on this page - int endRes; + idGraphics.setColor(Color.white); + idGraphics.fillRect(0, 0, pageWidth, pageHeight); + idGraphics.setFont(av.getFont()); - // /////////////////////////// - // / Only print these sequences and residues on this page - int startSeq; + /* + * How many sequences and residues can we fit on a printable page? + */ + final int totalRes = (pageWidth - idWidth) / av.getCharWidth(); - // /////////////////////////// - // / Only print these sequences and residues on this page - int endSeq; - startRes = (pi % pagesWide) * totalRes; - endRes = (startRes + totalRes) - 1; + final int totalSeq = (pageHeight - scaleHeight) / charHeight - 1; - if (endRes > (av.getAlignment().getWidth() - 1)) - { - endRes = av.getAlignment().getWidth() - 1; - } + final int alignmentWidth = av.getAlignment().getVisibleWidth(); + int pagesWide = (alignmentWidth / totalRes) + 1; - startSeq = (pi / pagesWide) * totalSeq; - endSeq = startSeq + totalSeq; + final int startRes = (pageIndex % pagesWide) * totalRes; + final int endRes = Math.min(startRes + totalRes - 1, + alignmentWidth - 1); - if (endSeq > av.getAlignment().getHeight()) - { - endSeq = av.getAlignment().getHeight(); - } + final int startSeq = (pageIndex / pagesWide) * totalSeq; + final int alignmentHeight = av.getAlignment().getHeight(); + final int endSeq = Math.min(startSeq + totalSeq, alignmentHeight); - int pagesHigh = ((av.getAlignment().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)) + if (pageIndex >= (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 - 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)) - { - currentColor = Color.gray; - currentTextColor = Color.black; - } - else - { - currentColor = av.getSequenceColour(seq); - currentTextColor = Color.black; - } - - pg.setColor(currentColor); - pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, - av.getCharHeight()); - - pg.setColor(currentTextColor); - - int xPos = 0; - if (av.rightAlignIds) - { - fm = pg.getFontMetrics(); - xPos = idWidth - - fm.stringWidth(seq.getDisplayId(av.getShowJVSuffix())) - - 4; - } - - pg.drawString( - seq.getDisplayId(av.getShowJVSuffix()), - xPos, - (((i - startSeq) * av.charHeight) + av.getCharHeight()) - - (av.getCharHeight() / 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.getAlignment().getHeight())) - { - pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3); - alabels.drawComponent((Graphics2D) pg, idWidth); - pg.translate(idWidth + 3, 0); - annotationPanel.renderer.drawComponent(annotationPanel, av, (Graphics2D) pg, -1, startRes, endRes + 1); + 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); + IdCanvas idCanvas = getIdPanel().getIdCanvas(); + List selection = av.getSelectionGroup() == null ? null + : av.getSelectionGroup().getSequences(null); + idCanvas.drawIds((Graphics2D) idGraphics, av, startSeq, endSeq - 1, + selection); + + 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 - 1); + alignmentGraphics.translate(-alignmentGraphicsOffset, 0); + + if (av.isShowAnnotation() && (endSeq == alignmentHeight)) + { + /* + * 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; } /** - * DOCUMENT ME! + * Prints one page of an alignment in wrapped mode. Returns + * Printable.PAGE_EXISTS (0) if a page was drawn, or Printable.NO_SUCH_PAGE if + * no page could be drawn (page number out of range). * - * @param pg - * DOCUMENT ME! - * @param pwidth - * DOCUMENT ME! - * @param pheight - * DOCUMENT ME! - * @param pi - * DOCUMENT ME! + * @param pageWidth + * @param pageHeight + * @param pageNumber + * (0, 1, ...) + * @param g * - * @return DOCUMENT ME! + * @return * * @throws PrinterException - * DOCUMENT ME! */ - public int printWrappedAlignment(Graphics pg, int pwidth, int pheight, - int pi) throws PrinterException + public int printWrappedAlignment(int pageWidth, int pageHeight, int pageNumber, + Graphics g) throws PrinterException { int annotationHeight = 0; - AnnotationLabels labels = null; - if (av.showAnnotation) + if (av.isShowAnnotation()) { - annotationHeight = annotationPanel.adjustPanelHeight(); - labels = new AnnotationLabels(av); + annotationHeight = getAnnotationPanel().adjustPanelHeight(); } - 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(false); - int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns()) - { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; - } + int maxwidth = av.getAlignment().getVisibleWidth(); - int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - - idWidth); + int resWidth = getSeqPanel().seqCanvas + .getWrappedCanvasWidth(pageWidth - idWidth); int totalHeight = cHeight * (maxwidth / resWidth + 1); - pg.setColor(Color.white); - pg.fillRect(0, 0, pwidth, pheight); - pg.setFont(av.getFont()); + g = g.create(); - // ////////////// - // Draw the ids - pg.setColor(Color.black); + g.setColor(Color.white); + g.fillRect(0, 0, pageWidth, pageHeight); + g.setFont(av.getFont()); + g.setColor(Color.black); - pg.translate(0, -pi * pheight); + /* + * method: print the whole wrapped alignment, but with a clip region that + * is restricted to the requested page; this supports selective print of + * single pages or ranges, (at the cost of some repeated processing in + * the 'normal' case, when all pages are printed) + */ + g.translate(0, -pageNumber * pageHeight); - pg.setClip(0, pi * pheight, pwidth, pheight); + // BH 2020.03.19 avoiding g.setClip + g.clipRect(0, pageNumber * pageHeight, pageWidth, pageHeight); - int ypos = hgap; + /* + * draw sequence ids and annotation labels (if shown) + */ + IdCanvas idCanvas = getIdPanel().getIdCanvas(); + idCanvas.drawIdsWrapped((Graphics2D) g, av, 0, totalHeight); - do - { - for (int i = 0; i < av.getAlignment().getHeight(); i++) - { - pg.setFont(idPanel.idCanvas.idfont); - SequenceI s = av.getAlignment().getSequenceAt(i); - String string = s.getDisplayId(av.getShowJVSuffix()); - int xPos = 0; - if (av.rightAlignIds) - { - FontMetrics fm = pg.getFontMetrics(); - xPos = idWidth - fm.stringWidth(string) - 4; - } - pg.drawString(string, xPos, - ((i * av.charHeight) + ypos + av.charHeight) - - (av.charHeight / 5)); - } - if (labels != null) - { - pg.translate(-3, ypos - + (av.getAlignment().getHeight() * av.charHeight)); + g.translate(idWidth, 0); - pg.setFont(av.getFont()); - labels.drawComponent(pg, idWidth); - pg.translate(+3, -ypos - - (av.getAlignment().getHeight() * av.charHeight)); - } - - ypos += cHeight; - } while (ypos < totalHeight); - - pg.translate(idWidth, 0); + getSeqPanel().seqCanvas.drawWrappedPanelForPrinting(g, pageWidth - idWidth, + totalHeight, 0); - seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, - 0); - - if ((pi * pheight) < totalHeight) + g.dispose(); + if ((pageNumber * pageHeight) < totalHeight) { return Printable.PAGE_EXISTS; - } else { return Printable.NO_SUCH_PAGE; } } + /** - * get current sequence ID panel width, or nominal value if panel were to be displayed using default settings + * get current sequence ID panel width, or nominal value if panel were to be + * displayed using default settings + * * @return */ - int getVisibleIdWidth() + public int getVisibleIdWidth() { return getVisibleIdWidth(true); } /** - * get current sequence ID panel width, or nominal value if panel were to be displayed using default settings - * @param onscreen indicate if the Id width for onscreen or offscreen display should be returned + * get current sequence ID panel width, or nominal value if panel were to be + * displayed using default settings + * + * @param onscreen + * indicate if the Id width for onscreen or offscreen display should + * be returned * @return */ - int getVisibleIdWidth(boolean onscreen) + public int getVisibleIdWidth(boolean onscreen) { // see if rendering offscreen - check preferences and calc width accordingly - if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false)) + if (!onscreen && Cache.getDefault(Preferences.FIGURE_AUTOIDWIDTH, false)) { - return calculateIdWidth(-1).width+4; + return calculateIdWidth(-1).width + 4; } - Integer idwidth=null; - if (onscreen || (idwidth=Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH"))==null) { - return (idPanel.getWidth() > 0 ? idPanel.getWidth() - : calculateIdWidth().width + 4); + Integer idwidth = null; + if (onscreen || (idwidth = Cache + .getIntegerProperty(Preferences.FIGURE_FIXEDIDWIDTH)) == null) + { + int w = getIdPanel().getWidth(); + return (w > 0 ? w : calculateIdWidth().width + 4); } - return idwidth.intValue()+4; + return idwidth.intValue() + 4; } - void makeAlignmentImage(int type, File file) + /** + * 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) { - int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns()) + final int borderBottomOffset = 5; + + AlignmentDimension aDimension = getAlignmentDimension(); + // todo use a lambda function in place of callback here? + ImageWriterI writer = new ImageWriterI() { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); - } + @Override + public void exportImage(Graphics graphics) throws Exception + { + 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); + } - int height = ((av.getAlignment().getHeight() + 1) * av.charHeight) - + scalePanel.getHeight(); - int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth); + /** + * Calculates and returns a suitable width and height (in pixels) for an + * exported image + * + * @return + */ + public AlignmentDimension getAlignmentDimension() + { + int maxwidth = av.getAlignment().getVisibleWidth(); + + int height = ((av.getAlignment().getHeight() + 1) * av.getCharHeight()) + + getScalePanel().getHeight(); + int width = getVisibleIdWidth(false) + (maxwidth * av.getCharWidth()); if (av.getWrapAlignment()) { height = getWrappedHeight(); - if (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true")) + if (Jalview.isHeadlessMode()) { - // need to obtain default alignment width and then add in any additional allowance for id margin - // this duplicates the calculation in getWrappedHeight but adjusts for offscreen idWith + // need to obtain default alignment width and then add in any + // additional allowance for id margin + // this duplicates the calculation in getWrappedHeight but adjusts for + // offscreen idWith width = alignFrame.getWidth() - vscroll.getPreferredSize().width - - alignFrame.getInsets().left - - alignFrame.getInsets().right - - getVisibleIdWidth()+getVisibleIdWidth(false); + - alignFrame.getInsets().left - alignFrame.getInsets().right + - getVisibleIdWidth() + getVisibleIdWidth(false); } else { - width = seqPanel.getWidth() + getVisibleIdWidth(false); + width = getSeqPanel().getWidth() + getVisibleIdWidth(false); } } - else if (av.getShowAnnotation()) - { - height += annotationPanel.adjustPanelHeight() + 3; - } - - try - { - - jalview.util.ImageMaker im; - if (type == jalview.util.ImageMaker.PNG) - { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.PNG, - "Create PNG image from alignment", width, height, file, - null); - } - else - { - im = new jalview.util.ImageMaker(this, jalview.util.ImageMaker.EPS, - "Create EPS file from alignment", width, height, file, - alignFrame.getTitle()); - } - - if (av.getWrapAlignment()) - { - if (im.getGraphics() != null) - { - printWrappedAlignment(im.getGraphics(), width, height, 0); - im.writeImage(); - } - } - else - { - if (im.getGraphics() != null) - { - printUnwrapped(im.getGraphics(), width, height, 0); - im.writeImage(); - } - } - } catch (OutOfMemoryError err) - { - // Be noisy here. - System.out.println("########################\n" + "OUT OF MEMORY " - + file + "\n" + "########################"); - new OOMWarning("Creating Image for " + file, err); - // System.out.println("Create IMAGE: " + err); - } catch (Exception ex) + else if (av.isShowAnnotation()) { - ex.printStackTrace(); + height += getAnnotationPanel().adjustPanelHeight() + 3; } - } + 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 + // /////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 // //////////////////////////////// @@ -1182,119 +1283,107 @@ public class AlignmentPanel extends GAlignmentPanel implements { try { - int s, sSize = av.getAlignment().getHeight(), res, alwidth = av.getAlignment() - .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(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.getAlignment().getSequenceAt(s); - SequenceFeature[] features = seq.getDatasetSequence() - .getSequenceFeatures(); SequenceGroup[] groups = av.getAlignment().findAllGroups(seq); - for (res = 0; res < alwidth; res++) + for (int column = 0; column < alwidth; column++) { - text = new StringBuffer(); - Object obj = null; + 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()); } } } @@ -1311,38 +1400,38 @@ public class AlignmentPanel extends GAlignmentPanel implements int getWrappedHeight() { - int seqPanelWidth = seqPanel.seqCanvas.getWidth(); + int seqPanelWidth = getSeqPanel().seqCanvas.getWidth(); - if (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true")) + if (Jalview.isHeadlessMode()) { seqPanelWidth = alignFrame.getWidth() - getVisibleIdWidth() - vscroll.getPreferredSize().width - alignFrame.getInsets().left - alignFrame.getInsets().right; } - int chunkWidth = seqPanel.seqCanvas + 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 + int cHeight = av.getAlignment().getHeight() * av.getCharHeight() + hgap + annotationHeight; 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; @@ -1356,15 +1445,32 @@ public class AlignmentPanel extends GAlignmentPanel implements */ public void closePanel() { - PaintRefresher.RemoveComponent(seqPanel.seqCanvas); - PaintRefresher.RemoveComponent(idPanel.idCanvas); + PaintRefresher.RemoveComponent(getSeqPanel().seqCanvas); + PaintRefresher.RemoveComponent(getIdPanel().getIdCanvas()); PaintRefresher.RemoveComponent(this); + + closeChildFrames(); + + /* + * try to ensure references are nulled + */ + if (annotationPanel != null) + { + annotationPanel.dispose(); + annotationPanel = null; + } + if (av != null) { - jalview.structure.StructureSelectionManager ssm = av.getStructureSelectionManager(); - ssm.removeStructureViewerListener(seqPanel, null); - ssm.removeSelectionListener(seqPanel); - av.setAlignment(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 @@ -1377,107 +1483,80 @@ public class AlignmentPanel extends GAlignmentPanel implements } /** + * 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); + updateAnnotation(false, false); } public void updateAnnotation(boolean applyGlobalSettings) { - // TODO: this should be merged with other annotation update stuff - that - // sits on AlignViewport - boolean updateCalcs = false; - boolean conv = av.isShowGroupConservation(); - boolean cons = av.isShowGroupConsensus(); - boolean showprf = av.isShowSequenceLogo(); - boolean showConsHist = av.isShowConsensusHistogram(); - boolean normLogo = av.isNormaliseSequenceLogo(); - - boolean sortg = true; - - // remove old automatic annotation - // add any new annotation - - // intersect alignment annotation with alignment groups + updateAnnotation(applyGlobalSettings, false); + } - AlignmentAnnotation[] aan = av.getAlignment().getAlignmentAnnotation(); - Hashtable oldrfs = new Hashtable(); - if (aan != null) - { - for (int an = 0; an < aan.length; an++) - { - if (aan[an].autoCalculated && aan[an].groupRef != null) - { - oldrfs.put(aan[an].groupRef, aan[an].groupRef); - av.getAlignment().deleteAnnotation(aan[an]); - aan[an] = null; - } - } - } - if (av.getAlignment().getGroups()!=null) - { - for (SequenceGroup sg:av.getAlignment().getGroups()) - { - updateCalcs = false; - if (applyGlobalSettings || !oldrfs.containsKey(sg)) - { - // set defaults for this group's conservation/consensus - sg.setshowSequenceLogo(showprf); - sg.setShowConsensusHistogram(showConsHist); - sg.setNormaliseSequenceLogo(normLogo); - } - if (conv) - { - updateCalcs = true; - av.getAlignment().addAnnotation(sg.getConservationRow(), 0); - } - if (cons) - { - updateCalcs = true; - av.getAlignment().addAnnotation(sg.getConsensus(), 0); - } - // refresh the annotation rows - if (updateCalcs) - { - sg.recalcConservation(); - } - } - } - oldrfs.clear(); + public void updateAnnotation(boolean applyGlobalSettings, + boolean preserveNewGroupSettings) + { + av.updateGroupAnnotationSettings(applyGlobalSettings, + preserveNewGroupSettings); adjustAnnotationHeight(); } @Override public AlignmentI getAlignment() { - return av.getAlignment(); + return av == null ? null : av.getAlignment(); } - /** - * get the name for this view - * @return - */ + @Override public String getViewName() { - return av.viewName; + return av.getViewName(); } /** * Make/Unmake this alignment panel the current input focus + * * @param b */ public void setSelected(boolean b) { - try { + 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) {}; - + } catch (Exception ex) + { + } + if (b) { alignFrame.setDisplayedView(this); - } + } } @Override @@ -1489,24 +1568,334 @@ public class AlignmentPanel extends GAlignmentPanel implements @Override public void raiseOOMWarning(String string, OutOfMemoryError error) { - new OOMWarning(string, error, this); + new OOMWarning(string, error, this); } - public FeatureRenderer cloneFeatureRenderer() + @Override + public jalview.api.FeatureRenderer cloneFeatureRenderer() { - + return new FeatureRenderer(this); } - public void updateFeatureRenderer(FeatureRenderer fr) + @Override + public jalview.api.FeatureRenderer getFeatureRenderer() { - fr.transferSettings(seqPanel.seqCanvas.getFeatureRenderer()); + return seqPanel.seqCanvas.getFeatureRenderer(); } - public void updateFeatureRendererFrom(FeatureRenderer fr) + public void updateFeatureRenderer( + jalview.renderer.seqfeatures.FeatureRenderer fr) { - if (seqPanel.seqCanvas.getFeatureRenderer()!=null) { - seqPanel.seqCanvas.getFeatureRenderer().transferSettings(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); + } + + /** + * 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; + } + + @Override + public SequenceRenderer getSequenceRenderer() + { + return seqPanel.seqCanvas.getSequenceRenderer(); + } + + public boolean scrollTo(int ostart, int end, int seqIndex, + boolean scrollToNearest, boolean redrawOverview) + { + int startv, endv, starts, ends;// , width; + + int start = -1; + if (av.hasHiddenColumns()) + { + AlignmentI al = av.getAlignment(); + start = al.getHiddenColumns().absoluteToVisibleColumn(ostart); + end = al.getHiddenColumns().absoluteToVisibleColumn(end); + if (start == end) + { + if (!scrollToNearest && !al.getHiddenColumns().isVisible(ostart)) + { + // don't scroll - position isn't visible + return false; + } + } + } + else + { + start = ostart; + } + + ViewportRanges ranges = av.getRanges(); + if (!av.getWrapAlignment()) + { + /* + * int spos=av.getStartRes(),sqpos=av.getStartSeq(); if ((startv = + * av.getStartRes()) >= start) { spos=start-1; // seqIn // + * setScrollValues(start - 1, seqIndex); } else if ((endv = + * av.getEndRes()) <= end) { // setScrollValues(spos=startv + 1 + end - + * endv, seqIndex); spos=startv + 1 + end - endv; } else if ((starts = + * av.getStartSeq()) > seqIndex) { setScrollValues(av.getStartRes(), + * seqIndex); } else if ((ends = av.getEndSeq()) <= seqIndex) { + * setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); } + */ + + // below is scrolling logic up to Jalview 2.8.2 + // if ((av.getStartRes() > end) + // || (av.getEndRes() < start) + // || ((av.getStartSeq() > seqIndex) || (av.getEndSeq() < seqIndex))) + // { + // if (start > av.getAlignment().getWidth() - hextent) + // { + // start = av.getAlignment().getWidth() - hextent; + // if (start < 0) + // { + // start = 0; + // } + // + // } + // if (seqIndex > av.getAlignment().getHeight() - vextent) + // { + // seqIndex = av.getAlignment().getHeight() - vextent; + // if (seqIndex < 0) + // { + // seqIndex = 0; + // } + // } + // setScrollValues(start, seqIndex); + // } + // logic copied from jalview.gui.AlignmentPanel: + if ((startv = ranges.getStartRes()) >= start) + { + /* + * Scroll left to make start of search results visible + */ + setScrollValues(start - 1, seqIndex); + } + else if ((endv = ranges.getEndRes()) <= end) + { + /* + * Scroll right to make end of search results visible + */ + setScrollValues(startv + 1 + 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 + */ + } + else + { + ranges.scrollToWrappedVisible(start); + } + + paintAlignment(redrawOverview, false); + return true; + } + + @Override + public void overviewDone(BufferedImage miniMe) + { + overviewPanel.canvas.finalizeDraw(miniMe); + } + + + private boolean holdRepaint = false; + + public boolean getHoldRepaint() + { + return holdRepaint; + } + + public void setHoldRepaint(boolean b) + { + if (holdRepaint == b) + { + return; + } + holdRepaint = b; + if (!b) + { + repaint(); + } + } + + @Override + public void repaint() + { + if (holdRepaint) + { + // System.out.println("AP repaint holding"); + // Platform.stackTrace(); + return; + } + super.repaint(); + } + }