X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignmentPanel.java;h=e1b5abb3c2e6571347faec893b4acb813d0d058f;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;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..e1b5abb --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -1,66 +1,100 @@ /* - * 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 2.8.2b1) + * Copyright (C) 2014 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.AlignmentViewPanel; +import jalview.bin.Cache; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SearchResults; +import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceGroup; +import jalview.datamodel.SequenceI; +import jalview.jbgui.GAlignmentPanel; +import jalview.schemes.ResidueProperties; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; + +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Container; +import java.awt.Dimension; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.event.AdjustmentEvent; +import java.awt.event.AdjustmentListener; +import java.awt.print.PageFormat; +import java.awt.print.Printable; +import java.awt.print.PrinterException; +import java.beans.PropertyChangeEvent; +import java.beans.PropertyChangeListener; +import java.io.File; +import java.io.FileWriter; +import java.io.PrintWriter; + +import javax.swing.SwingUtilities; /** * DOCUMENT ME! - * + * * @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 { public AlignViewport av; + OverviewPanel overviewPanel; + SeqPanel seqPanel; + 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; /** * Creates a new AlignmentPanel object. - * - * @param af DOCUMENT ME! - * @param av DOCUMENT ME! + * + * @param af + * DOCUMENT ME! + * @param av + * DOCUMENT ME! */ public AlignmentPanel(AlignFrame af, final AlignViewport av) { @@ -98,15 +132,11 @@ public class AlignmentPanel { if (evt.getPropertyName().equals("alignment")) { - PaintRefresher.Refresh(ap, - av.getSequenceSetId(), - true, - true); + PaintRefresher.Refresh(ap, av.getSequenceSetId(), true, true); alignmentChanged(); } } }); - fontChanged(); adjustAnnotationHeight(); @@ -131,10 +161,10 @@ 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())); + 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; @@ -154,25 +184,44 @@ public class AlignmentPanel } /** - * 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 + + int afwidth = (alignFrame != null ? alignFrame.getWidth() : 300); + int maxwidth = Math.max(20, + Math.min(afwidth - 200, 2 * afwidth / 3)); + return calculateIdWidth(maxwidth); + } + + /** + * Calculate the width of the alignment labels based on the displayed names + * and any bounds on label width set in preferences. + * + * @param maxwidth + * -1 or maximum width allowed for IdWidth + * @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())); + FontMetrics fm = c.getFontMetrics(new Font(av.font.getName(), + Font.ITALIC, av.font.getSize())); AlignmentI al = av.getAlignment(); - int afwidth = (alignFrame!=null ? alignFrame.getWidth() : 300); - int maxwidth = Math.max(20,Math.min(afwidth-200,(int) 2*afwidth/3)); int i = 0; int idWidth = 0; String id; - while ( (i < al.getHeight()) && (al.getSequenceAt(i) != null)) + while ((i < al.getHeight()) && (al.getSequenceAt(i) != null)) { SequenceI s = al.getSequenceAt(i); @@ -206,32 +255,105 @@ 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(SearchResults results) { + scrollToPosition(results); seqPanel.seqCanvas.highlightSearchResults(results); + } + /** + * scroll the view to show the position of the highlighted region in results + * (if any) and redraw the overview + * + * @param results + */ + public boolean scrollToPosition(SearchResults results) + { + return scrollToPosition(results, true); + } + + /** + * scroll the view to show the position of the highlighted region in results + * (if any) + * + * @param results + * @param redrawOverview + * - when set, the overview will be recalculated (takes longer) + * @return false if results were not found + */ + 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? - if (results != null) + // TODO: tons of nullpointereexceptions raised here. + if (results != null && results.getSize() > 0 && av != null + && av.getAlignment() != 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; + 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) + { + return false; + } + if (end == seq.getEnd()) + { + return false; + } + if (av.hasHiddenColumns()) + { + start = av.getColumnSelection().findColumnPosition(start); + end = av.getColumnSelection().findColumnPosition(end); + if (start == end) + { + if (!av.getColumnSelection().isVisible(r[0])) + { + // don't scroll - position isn't visible + return false; + } + } + } if (!av.wrapAlignment) { - if ( (av.getStartRes() > end) || (av.getEndRes() < start) || - ( (av.getStartSeq() > seqIndex) || (av.getEndSeq() < 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(start, seqIndex); + setScrollValues(av.getStartRes(), starts + seqIndex - ends + 1); } } else @@ -239,24 +361,29 @@ public class AlignmentPanel scrollToWrappedVisible(start); } } - - paintAlignment(true); + if (redrawOverview && overviewPanel != null) + { + overviewPanel.setBoxPosition(); + } + paintAlignment(redrawOverview); + return true; } void scrollToWrappedVisible(int res) { - int cwidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas. - getWidth()); - if (res <= av.getStartRes() || res >= (av.getStartRes() + cwidth)) + int cwidth = seqPanel.seqCanvas + .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); + if (res < av.getStartRes() || res >= (av.getStartRes() + cwidth)) { - vscroll.setValue(res / cwidth); + vscroll.setValue((res / cwidth)); av.startRes = vscroll.getValue() * cwidth; } + } /** * DOCUMENT ME! - * + * * @return DOCUMENT ME! */ public OverviewPanel getOverviewPanel() @@ -266,8 +393,9 @@ public class AlignmentPanel /** * DOCUMENT ME! - * - * @param op DOCUMENT ME! + * + * @param op + * DOCUMENT ME! */ public void setOverviewPanel(OverviewPanel op) { @@ -275,9 +403,10 @@ public class AlignmentPanel } /** - * DOCUMENT ME! - * - * @param b DOCUMENT ME! + * + * @param b + * Hide or show annotation panel + * */ public void setAnnotationVisible(boolean b) { @@ -289,43 +418,78 @@ public class AlignmentPanel repaint(); } + /** + * automatically adjust annotation panel height for new annotation whilst + * ensuring the alignment is still visible. + */ public void adjustAnnotationHeight() { - //TODO: display vertical annotation scrollbar if necessary + // 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(); + paintAlignment(true); + } + /** + * calculate the annotation dimensions and refresh slider values accordingly. + * need to do repaints/notifys afterwards. + */ + protected void validateAnnotationDimensions(boolean adjustPanelHeight) + { int height = annotationPanel.adjustPanelHeight(); - if (hscroll.isVisible()) + int theight = av.getCharHeight() + * (av.getAlignment().getHeight() + (!av.hasHiddenRows() ? 0 + : av.getAlignment().getHiddenSequences().getSize())); + float sscaling = (float) (theight / (1.0 * theight + height)); + float ascaling = (float) (height * 1.0 / alignFrame.getHeight()); + int rheight = alignFrame.getHeight() - height - av.getCharHeight(); + if (adjustPanelHeight) { - height += hscroll.getPreferredSize().height; + // NOTE: this logic is different in the applet. Need a better algorithm to + // define behaviour + // try and set height according to alignment + if (ascaling > 0 && sscaling < 0.5) + { + // if the alignment is too big then + // default is 0.5 split + height = alignFrame.getHeight() / 2; + } + else + { + // if space for more than one sequence row left when annotation is fully + // displayed then set height to annotation height + // otherwise, leave at least two lines of sequence shown. + height = (rheight > av.getCharHeight()) ? height + : (-av.getCharHeight() * 3 + (int) (alignFrame.getHeight() * (1 - sscaling))); + } } - if (height > alignFrame.getHeight() / 2) + else { - height = alignFrame.getHeight() / 2; + // maintain same window layout whilst updating sliders + height = annotationScroller.getSize().height; } - hscroll.addNotify(); - annotationScroller.setPreferredSize( - new Dimension(annotationScroller.getWidth(), height)); - + annotationScroller.setPreferredSize(new Dimension(annotationScroller + .getWidth(), height)); annotationSpaceFillerHolder.setPreferredSize(new Dimension( - annotationSpaceFillerHolder.getWidth(), - height)); + annotationSpaceFillerHolder.getWidth(), height)); annotationScroller.validate();// repaint(); - repaint(); + annotationScroller.addNotify(); } /** * DOCUMENT ME! - * - * @param wrap DOCUMENT ME! + * + * @param wrap + * DOCUMENT ME! */ public void setWrapAlignment(boolean wrap) { @@ -365,7 +529,7 @@ public class AlignmentPanel } else { - if ( (vextent + vscroll.getValue()) >= av.getAlignment().getHeight()) + if ((vextent + vscroll.getValue()) >= av.getAlignment().getHeight()) { return false; } @@ -381,9 +545,10 @@ public class AlignmentPanel /** * DOCUMENT ME! - * - * @param right DOCUMENT ME! - * + * + * @param right + * DOCUMENT ME! + * * @return DOCUMENT ME! */ public boolean scrollRight(boolean right) @@ -400,7 +565,7 @@ public class AlignmentPanel } else { - if ( (hextent + hscroll.getValue()) >= av.getAlignment().getWidth()) + if ((hextent + hscroll.getValue()) >= av.getAlignment().getWidth()) { return false; } @@ -415,23 +580,30 @@ public class AlignmentPanel } /** - * DOCUMENT ME! - * - * @param x DOCUMENT ME! - * @param y DOCUMENT ME! + * Adjust row/column scrollers to show a visible position in the alignment. + * + * @param x + * visible column to scroll to DOCUMENT ME! + * @param y + * visible row to scroll to + * */ public void setScrollValues(int x, int y) { + // System.err.println("Scroll to "+x+","+y); + if (av == null || av.getAlignment() == null) + { + return; + } + int width = av.getAlignment().getWidth(); + int height = av.getAlignment().getHeight(); - int width = av.alignment.getWidth(); - int height = av.alignment.getHeight(); - - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { width = av.getColumnSelection().findColumnPosition(width); } - av.setEndRes( (x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1); + av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.charWidth)) - 1); hextent = seqPanel.seqCanvas.getWidth() / av.charWidth; vextent = seqPanel.seqCanvas.getHeight() / av.charHeight; @@ -446,12 +618,12 @@ public class AlignmentPanel vextent = height; } - if ( (hextent + x) > width) + if ((hextent + x) > width) { x = width - hextent; } - if ( (vextent + y) > height) + if ((vextent + y) > height) { y = height - vextent; } @@ -472,8 +644,9 @@ public class AlignmentPanel /** * DOCUMENT ME! - * - * @param evt DOCUMENT ME! + * + * @param evt + * DOCUMENT ME! */ public void adjustmentValueChanged(AdjustmentEvent evt) { @@ -485,8 +658,7 @@ public class AlignmentPanel { int x = hscroll.getValue(); av.setStartRes(x); - av.setEndRes( (x + - (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1); + av.setEndRes((x + (seqPanel.seqCanvas.getWidth() / av.getCharWidth())) - 1); } if (evt.getSource() == vscroll) @@ -497,16 +669,16 @@ public class AlignmentPanel { if (offy > -1) { - int rowSize = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel. - seqCanvas.getWidth()); + int rowSize = seqPanel.seqCanvas + .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); av.setStartRes(offy * rowSize); - av.setEndRes( (offy + 1) * 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 + // 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() @@ -519,8 +691,8 @@ public class AlignmentPanel else { av.setStartSeq(offy); - av.setEndSeq(offy + - (seqPanel.seqCanvas.getHeight() / av.getCharHeight())); + av.setEndSeq(offy + + (seqPanel.seqCanvas.getHeight() / av.getCharHeight())); } } @@ -552,11 +724,10 @@ public class AlignmentPanel if (scrollX != 0 || scrollY != 0) { idPanel.idCanvas.fastPaint(scrollY); - seqPanel.seqCanvas.fastPaint(scrollX, - scrollY); + seqPanel.seqCanvas.fastPaint(scrollX, scrollY); scalePanel.repaint(); - if (av.getShowAnnotation()) + if (av.getShowAnnotation() && scrollX != 0) { annotationPanel.fastPaint(scrollX); } @@ -564,14 +735,22 @@ public class AlignmentPanel } } + /** + * Repaint the alignment including the annotations and overview panels (if + * shown). + */ public void paintAlignment(boolean updateOverview) { + final AnnotationSorter sorter = new AnnotationSorter(getAlignment(), + av.isShowAutocalculatedAbove()); + sorter.sort(getAlignment() + .getAlignmentAnnotation(), + av.getSortAnnotationsBy()); repaint(); - if(updateOverview) + if (updateOverview) { - jalview.structure.StructureSelectionManager.getStructureSelectionManager() - .sequenceColoursChanged(this); + av.getStructureSelectionManager().sequenceColoursChanged(this); if (overviewPanel != null) { @@ -582,8 +761,9 @@ public class AlignmentPanel /** * DOCUMENT ME! - * - * @param g DOCUMENT ME! + * + * @param g + * DOCUMENT ME! */ public void paintComponent(Graphics g) { @@ -596,21 +776,21 @@ public class AlignmentPanel if (av.getWrapAlignment()) { - int maxwidth = av.alignment.getWidth(); + int maxwidth = av.getAlignment().getWidth(); - if (av.hasHiddenColumns) + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } - int canvasWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel. - seqCanvas.getWidth()); + int canvasWidth = seqPanel.seqCanvas + .getWrappedCanvasWidth(seqPanel.seqCanvas.getWidth()); if (canvasWidth > 0) { - int max = maxwidth / - seqPanel.seqCanvas.getWrappedCanvasWidth(seqPanel.seqCanvas. - getWidth()) + - 1; + int max = maxwidth + / seqPanel.seqCanvas + .getWrappedCanvasWidth(seqPanel.seqCanvas + .getWidth()) + 1; vscroll.setMaximum(max); vscroll.setUnitIncrement(1); vscroll.setVisibleAmount(1); @@ -624,19 +804,23 @@ public class AlignmentPanel /** * 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! */ 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(); @@ -653,20 +837,25 @@ 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 printUnwrapped(Graphics pg, int pwidth, int pheight, int pi) - throws PrinterException + throws PrinterException { - int idWidth = getVisibleIdWidth(); + int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); int scaleHeight = av.charHeight + fm.getDescent(); @@ -674,29 +863,28 @@ public class AlignmentPanel pg.fillRect(0, 0, pwidth, pheight); pg.setFont(av.getFont()); - //////////////////////////////////// - /// How many sequences and residues can we fit on a printable page? + // ////////////////////////////////// + // / How many sequences and residues can we fit on a printable page? int totalRes = (pwidth - idWidth) / av.getCharWidth(); - int totalSeq = (int) ( (pheight - scaleHeight) / av.getCharHeight()) - - 1; + int totalSeq = (pheight - scaleHeight) / av.getCharHeight() - 1; int pagesWide = (av.getAlignment().getWidth() / totalRes) + 1; - ///////////////////////////// - /// Only print these sequences and residues on this page + // /////////////////////////// + // / Only print these sequences and residues on this page int startRes; - ///////////////////////////// - /// Only print these sequences and residues on this page + // /////////////////////////// + // / Only print these sequences and residues on this page int endRes; - ///////////////////////////// - /// Only print these sequences and residues on this page + // /////////////////////////// + // / Only print these sequences and residues on this page int startSeq; - ///////////////////////////// - /// Only print these sequences and residues on this page + // /////////////////////////// + // / Only print these sequences and residues on this page int endSeq; startRes = (pi % pagesWide) * totalRes; endRes = (startRes + totalRes) - 1; @@ -714,7 +902,8 @@ public class AlignmentPanel endSeq = av.getAlignment().getHeight(); } - int pagesHigh = ( (av.alignment.getHeight() / totalSeq) + 1) * pheight; + int pagesHigh = ((av.getAlignment().getHeight() / totalSeq) + 1) + * pheight; if (av.showAnnotation) { @@ -728,12 +917,13 @@ public class AlignmentPanel return Printable.NO_SUCH_PAGE; } - //draw Scale + // draw Scale pg.translate(idWidth, 0); - scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, scaleHeight); - pg.translate( -idWidth, scaleHeight); + scalePanel.drawScale(pg, startRes, endRes, pwidth - idWidth, + scaleHeight); + pg.translate(-idWidth, scaleHeight); - //////////////// + // ////////////// // Draw the ids Color currentColor = null; Color currentTextColor = null; @@ -744,8 +934,8 @@ public class AlignmentPanel 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)) { currentColor = Color.gray; currentTextColor = Color.black; @@ -758,7 +948,7 @@ public class AlignmentPanel pg.setColor(currentColor); pg.fillRect(0, (i - startSeq) * av.charHeight, idWidth, - av.getCharHeight()); + av.getCharHeight()); pg.setColor(currentTextColor); @@ -766,15 +956,16 @@ public class AlignmentPanel if (av.rightAlignIds) { fm = pg.getFontMetrics(); - xPos = idWidth - fm.stringWidth( - seq.getDisplayId(av.getShowJVSuffix()) - ) - 4; + 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.drawString( + seq.getDisplayId(av.getShowJVSuffix()), + xPos, + (((i - startSeq) * av.charHeight) + av.getCharHeight()) + - (av.getCharHeight() / 5)); } pg.setFont(av.getFont()); @@ -783,13 +974,17 @@ public class AlignmentPanel pg.translate(idWidth, 0); seqPanel.seqCanvas.drawPanel(pg, startRes, endRes, startSeq, endSeq, 0); - if (av.showAnnotation && (endSeq == av.alignment.getHeight())) + if (av.showAnnotation && (endSeq == av.getAlignment().getHeight())) { - pg.translate( -idWidth - 3, (endSeq - startSeq) * av.charHeight + 3); - alabels.drawComponent( (Graphics2D) pg, idWidth); + // draw annotation - need to offset for current scroll position + int offset = -alabels.scrollOffset; + pg.translate(0, offset); + pg.translate(-idWidth - 3, (endSeq - startSeq) * av.charHeight + 3); + alabels.drawComponent(pg, idWidth); pg.translate(idWidth + 3, 0); - annotationPanel.drawComponent( (Graphics2D) pg, startRes, endRes + - 1); + annotationPanel.renderer.drawComponent(annotationPanel, av, + pg, -1, startRes, endRes + 1); + pg.translate(0, -offset); } return Printable.PAGE_EXISTS; @@ -797,19 +992,23 @@ 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 + int pi) throws PrinterException { int annotationHeight = 0; @@ -826,20 +1025,19 @@ public class AlignmentPanel hgap += av.charHeight; } - int cHeight = av.getAlignment().getHeight() * av.charHeight - + hgap - + annotationHeight; + int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + + annotationHeight; - int idWidth = getVisibleIdWidth(); + int idWidth = getVisibleIdWidth(false); - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } - int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth - - idWidth); + int resWidth = seqPanel.seqCanvas.getWrappedCanvasWidth(pwidth + - idWidth); int totalHeight = cHeight * (maxwidth / resWidth + 1); @@ -847,7 +1045,7 @@ public class AlignmentPanel pg.fillRect(0, 0, pwidth, pheight); pg.setFont(av.getFont()); - //////////////// + // ////////////// // Draw the ids pg.setColor(Color.black); @@ -859,10 +1057,10 @@ 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); + SequenceI s = av.getAlignment().getSequenceAt(i); String string = s.getDisplayId(av.getShowJVSuffix()); int xPos = 0; if (av.rightAlignIds) @@ -871,31 +1069,29 @@ public class AlignmentPanel xPos = idWidth - fm.stringWidth(string) - 4; } pg.drawString(string, xPos, - ( (i * av.charHeight) + ypos + av.charHeight) - - (av.charHeight / 5)); + ((i * av.charHeight) + ypos + av.charHeight) + - (av.charHeight / 5)); } if (labels != null) { - pg.translate( -3, - ypos + - (av.getAlignment().getHeight() * av.charHeight)); + pg.translate(-3, ypos + + (av.getAlignment().getHeight() * av.charHeight)); 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.charHeight)); } ypos += cHeight; - } - while (ypos < totalHeight); + } while (ypos < totalHeight); pg.translate(idWidth, 0); - seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, 0); + seqPanel.seqCanvas.drawWrappedPanel(pg, pwidth - idWidth, totalHeight, + 0); - if ( (pi * pheight) < totalHeight) + if ((pi * pheight) < totalHeight) { return Printable.PAGE_EXISTS; @@ -906,103 +1102,148 @@ public class AlignmentPanel } } + /** + * get current sequence ID panel width, or nominal value if panel were to be + * displayed using default settings + * + * @return + */ 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 + */ + int getVisibleIdWidth(boolean onscreen) { - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + // see if rendering offscreen - check preferences and calc width accordingly + if (!onscreen && Cache.getDefault("FIGURE_AUTOIDWIDTH", false)) { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); + return calculateIdWidth(-1).width + 4; } - - int height = ( (av.alignment.getHeight() + 1) * av.charHeight) - + scalePanel.getHeight(); - int width = getVisibleIdWidth() + (maxwidth * av.charWidth); - - if (av.getWrapAlignment()) + Integer idwidth = null; + if (onscreen + || (idwidth = Cache.getIntegerProperty("FIGURE_FIXEDIDWIDTH")) == null) { - height = getWrappedHeight(); - if (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true")) - { - width = alignFrame.getWidth() - - vscroll.getPreferredSize().width - - alignFrame.getInsets().left - - alignFrame.getInsets().right; - } - else - { - width = seqPanel.getWidth() + getVisibleIdWidth(); - } - + return (idPanel.getWidth() > 0 ? idPanel.getWidth() + : calculateIdWidth().width + 4); } - else if (av.getShowAnnotation()) + return idwidth.intValue() + 4; + } + + void makeAlignmentImage(jalview.util.ImageMaker.TYPE type, File file) + { + long progress = System.currentTimeMillis(); + boolean headless = (System.getProperty("java.awt.headless") != null && System + .getProperty("java.awt.headless").equals("true")); + if (alignFrame != null && !headless) { - height += annotationPanel.adjustPanelHeight() + 3; + alignFrame.setProgressBar(MessageManager.formatMessage( + "status.saving_file", + new String[] + { type.getLabel() }), progress); } - try { - - jalview.util.ImageMaker im; - if (type == jalview.util.ImageMaker.PNG) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { - 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()); + maxwidth = av.getColumnSelection().findColumnPosition(maxwidth); } + int height = ((av.getAlignment().getHeight() + 1) * av.charHeight) + + scalePanel.getHeight(); + int width = getVisibleIdWidth(false) + (maxwidth * av.charWidth); + if (av.getWrapAlignment()) { - if (im.getGraphics() != null) + height = getWrappedHeight(); + if (headless) { - printWrappedAlignment(im.getGraphics(), width, height, 0); - im.writeImage(); + // need to obtain default alignment width and then add in any + // additional allowance for id margin + // this duplicates the calculation in getWrappedHeight but adjusts for + // offscreen idWith + width = alignFrame.getWidth() - vscroll.getPreferredSize().width + - alignFrame.getInsets().left + - alignFrame.getInsets().right - getVisibleIdWidth() + + getVisibleIdWidth(false); } + else + { + width = seqPanel.getWidth() + getVisibleIdWidth(false); + } + } - else + else if (av.getShowAnnotation()) + { + height += annotationPanel.adjustPanelHeight() + 3; + } + + try { - if (im.getGraphics() != null) + + jalview.util.ImageMaker im; + final String imageAction, imageTitle; + if (type == jalview.util.ImageMaker.TYPE.PNG) { - printUnwrapped(im.getGraphics(), width, height, 0); - im.writeImage(); + imageAction = "Create PNG image from alignment"; + imageTitle = null; + } + else if (type == jalview.util.ImageMaker.TYPE.EPS) + { + imageAction = "Create EPS file from alignment"; + imageTitle = alignFrame.getTitle(); + } + else + { + imageAction = "Create SVG file from alignment"; + imageTitle = alignFrame.getTitle(); } - } - } - catch (OutOfMemoryError err) - { - 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(); - } - catch (Exception ex) + im = new jalview.util.ImageMaker(this, type, imageAction, width, + height, file, imageTitle); + if (av.getWrapAlignment()) + { + if (im.getGraphics() != null) + { + printWrappedAlignment(im.getGraphics(), width, height, 0); + im.writeImage(); + } + } + else + { + if (im.getGraphics() != null) + { + printUnwrapped(im.getGraphics(), width, height, 0); + im.writeImage(); + } + } + } catch (OutOfMemoryError err) + { + // Be noisy here. + System.out.println("########################\n" + "OUT OF MEMORY " + + file + "\n" + "########################"); + new OOMWarning("Creating Image for " + file, err); + // System.out.println("Create IMAGE: " + err); + } catch (Exception ex) + { + ex.printStackTrace(); + } + } finally { - ex.printStackTrace(); + if (alignFrame != null && !headless) + { + alignFrame.setProgressBar(MessageManager.getString("status.export_complete"), progress); + } } } @@ -1011,7 +1252,7 @@ public class AlignmentPanel */ public void makeEPS(File epsFile) { - makeAlignmentImage(jalview.util.ImageMaker.EPS, epsFile); + makeAlignmentImage(jalview.util.ImageMaker.TYPE.EPS, epsFile); } /** @@ -1019,53 +1260,57 @@ public class AlignmentPanel */ public void makePNG(File pngFile) { - makeAlignmentImage(jalview.util.ImageMaker.PNG, pngFile); + makeAlignmentImage(jalview.util.ImageMaker.TYPE.PNG, pngFile); } + public void makeSVG(File svgFile) + { + makeAlignmentImage(jalview.util.ImageMaker.TYPE.SVG, svgFile); + } public void makePNGImageMap(File imgMapFile, String imageName) { - ///////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS - ////////////////////////////////////////////// - int idWidth = getVisibleIdWidth(); + // /////ONLY WORKS WITH NONE WRAPPED ALIGNMENTS + // //////////////////////////////////////////// + int idWidth = getVisibleIdWidth(false); FontMetrics fm = getFontMetrics(av.getFont()); int scaleHeight = av.charHeight + 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; + int s, sSize = av.getAlignment().getHeight(), res, alwidth = av + .getAlignment().getWidth(), g, gSize, f, fSize, sy; StringBuffer text = new StringBuffer(); PrintWriter out = new PrintWriter(new FileWriter(imgMapFile)); out.println(jalview.io.HTMLOutput.getImageMapHTML()); - out.println("" - + ""); + out.println("" + + ""); for (s = 0; s < sSize; s++) { sy = s * av.charHeight + scaleHeight; - SequenceI seq = av.alignment.getSequenceAt(s); - SequenceFeature[] features = seq.getDatasetSequence(). - getSequenceFeatures(); - SequenceGroup[] groups = av.alignment.findAllGroups(seq); + SequenceI seq = av.getAlignment().getSequenceAt(s); + SequenceFeature[] features = seq.getDatasetSequence() + .getSequenceFeatures(); + SequenceGroup[] groups = av.getAlignment().findAllGroups(seq); for (res = 0; res < alwidth; res++) { text = new StringBuffer(); Object obj = null; - if (av.alignment.isNucleotide()) + if (av.getAlignment().isNucleotide()) { - obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) + - ""); + obj = ResidueProperties.nucleotideName.get(seq.getCharAt(res) + + ""); } else { - obj = ResidueProperties.aa2Triplet.get( - seq.getCharAt(res) + ""); + obj = ResidueProperties.aa2Triplet.get(seq.getCharAt(res) + + ""); } if (obj == null) @@ -1081,15 +1326,15 @@ public class AlignmentPanel if (text.length() < 1) { text.append(" res) + if (groups[g].getStartRes() < res + && groups[g].getEndRes() > res) { text.append("
" + groups[g].getName() + ""); } @@ -1100,44 +1345,45 @@ public class AlignmentPanel if (text.length() < 1) { text.append("= seq.findPosition(res))) + if ((features[f].getBegin() <= seq.findPosition(res)) + && (features[f].getEnd() >= seq.findPosition(res))) { if (features[f].getType().equals("disulfide bond")) { if (features[f].getBegin() == seq.findPosition(res) - || features[f].getEnd() == seq.findPosition(res)) + || features[f].getEnd() == seq + .findPosition(res)) { - text.append("
disulfide bond " + features[f].getBegin() + - ":" + - features[f].getEnd()); + text.append("
disulfide bond " + + features[f].getBegin() + ":" + + features[f].getEnd()); } } else { text.append("
"); text.append(features[f].getType()); - if (features[f].getDescription() != null && - !features[f]. - getType().equals(features[f].getDescription())) + 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") + ")"); + text.append(" (" + features[f].getValue("status") + + ")"); } } } @@ -1154,12 +1400,11 @@ public class AlignmentPanel out.println(""); out.close(); - } - catch (Exception ex) + } catch (Exception ex) { ex.printStackTrace(); } - } ///////////END OF IMAGE MAP + } // /////////END OF IMAGE MAP } @@ -1168,18 +1413,15 @@ public class AlignmentPanel int seqPanelWidth = seqPanel.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 = seqPanel.seqCanvas + .getWrappedCanvasWidth(seqPanelWidth); int hgap = av.charHeight; if (av.scaleAboveWrapped) @@ -1193,18 +1435,130 @@ public class AlignmentPanel annotationHeight = annotationPanel.adjustPanelHeight(); } - int cHeight = av.getAlignment().getHeight() * av.charHeight - + hgap - + annotationHeight; + int cHeight = av.getAlignment().getHeight() * av.charHeight + hgap + + annotationHeight; - int maxwidth = av.alignment.getWidth(); - if (av.hasHiddenColumns) + int maxwidth = av.getAlignment().getWidth(); + if (av.hasHiddenColumns()) { maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; } - 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(seqPanel.seqCanvas); + PaintRefresher.RemoveComponent(idPanel.idCanvas); + PaintRefresher.RemoveComponent(this); + if (av != null) + { + jalview.structure.StructureSelectionManager ssm = av + .getStructureSelectionManager(); + ssm.removeStructureViewerListener(seqPanel, null); + ssm.removeSelectionListener(seqPanel); + av.setAlignment(null); + av = null; + } + else + { + if (Cache.log.isDebugEnabled()) + { + Cache.log.warn("Closing alignment panel which is already closed."); + } + } + } + + /** + * 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.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 + { + 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); + } + + public FeatureRenderer cloneFeatureRenderer() + { + + return new FeatureRenderer(this); + } + + public void updateFeatureRenderer(FeatureRenderer fr) + { + fr.transferSettings(seqPanel.seqCanvas.getFeatureRenderer()); + } + + public void updateFeatureRendererFrom(FeatureRenderer fr) + { + if (seqPanel.seqCanvas.getFeatureRenderer() != null) + { + seqPanel.seqCanvas.getFeatureRenderer().transferSettings(fr); + } + } }