X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdCanvas.java;h=793c005ed861d9bbf37f26bab3cb01b8f8628475;hb=78f5bbe9330cbf3d686d1a5c411956e091c88541;hp=7ccc3790f5a890e27c77aed439755f952c54c991;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/gui/IdCanvas.java b/src/jalview/gui/IdCanvas.java index 7ccc379..793c005 100755 --- a/src/jalview/gui/IdCanvas.java +++ b/src/jalview/gui/IdCanvas.java @@ -1,28 +1,41 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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 - * of the License, or (at your option) any later version. + * This file is part of Jalview. * - * 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 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. + * + * 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.awt.*; -import java.awt.image.*; -import javax.swing.*; +import jalview.datamodel.SequenceI; +import jalview.viewmodel.ViewportListenerI; +import jalview.viewmodel.ViewportRanges; -import jalview.datamodel.*; +import java.awt.BorderLayout; +import java.awt.Color; +import java.awt.Font; +import java.awt.FontMetrics; +import java.awt.Graphics; +import java.awt.Graphics2D; +import java.awt.RenderingHints; +import java.awt.image.BufferedImage; +import java.beans.PropertyChangeEvent; +import java.util.List; + +import javax.swing.JPanel; /** * DOCUMENT ME! @@ -30,7 +43,7 @@ import jalview.datamodel.*; * @author $author$ * @version $Revision$ */ -public class IdCanvas extends JPanel +public class IdCanvas extends JPanel implements ViewportListenerI { protected AlignViewport av; @@ -48,85 +61,85 @@ public class IdCanvas extends JPanel boolean fastPaint = false; - java.util.Vector searchResults; - - FontMetrics fm; - - AnnotationLabels labels = null; + List searchResults; AnnotationPanel ap; - Font idfont; + private Font idfont; /** * Creates a new IdCanvas object. * * @param av - * DOCUMENT ME! + * DOCUMENT ME! */ public IdCanvas(AlignViewport av) { setLayout(new BorderLayout()); this.av = av; PaintRefresher.Register(this, av.getSequenceSetId()); - } + av.getRanges().addPropertyChangeListener(this); + } /** * DOCUMENT ME! * - * @param gg - * DOCUMENT ME! + * @param g + * DOCUMENT ME! + * @param hiddenRows + * true - check and display hidden row marker if need be * @param s - * DOCUMENT ME! + * DOCUMENT ME! * @param i - * DOCUMENT ME! + * DOCUMENT ME! * @param starty - * DOCUMENT ME! + * DOCUMENT ME! * @param ypos - * DOCUMENT ME! + * DOCUMENT ME! */ - public void drawIdString(Graphics2D gg, SequenceI s, int i, int starty, - int ypos) + public void drawIdString(Graphics2D g, boolean hiddenRows, SequenceI s, + int i, int starty, int ypos) { int xPos = 0; int panelWidth = getWidth(); - int charHeight = av.charHeight; + int charHeight = av.getCharHeight(); if ((searchResults != null) && searchResults.contains(s)) { - gg.setColor(Color.black); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + g.setColor(Color.black); + g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), charHeight); - gg.setColor(Color.white); + g.setColor(Color.white); } else if ((av.getSelectionGroup() != null) && av.getSelectionGroup().getSequences(null).contains(s)) { - gg.setColor(Color.lightGray); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + g.setColor(Color.lightGray); + g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), charHeight); - gg.setColor(Color.white); + g.setColor(Color.white); } else { - gg.setColor(av.getSequenceColour(s)); - gg.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), + g.setColor(av.getSequenceColour(s)); + g.fillRect(0, ((i - starty) * charHeight) + ypos, getWidth(), charHeight); - gg.setColor(Color.black); + g.setColor(Color.black); } - if (av.rightAlignIds) + if (av.isRightAlignIds()) { + FontMetrics fm = g.getFontMetrics(); xPos = panelWidth - fm.stringWidth(s.getDisplayId(av.getShowJVSuffix())) - 4; } - gg.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos, + g.drawString(s.getDisplayId(av.getShowJVSuffix()), xPos, (((i - starty + 1) * charHeight) + ypos) - (charHeight / 5)); - if (av.hasHiddenRows && av.showHiddenMarkers) + if (hiddenRows) { - drawMarker(i, starty, ypos); + drawMarker(g, av, i, starty, ypos); } } @@ -135,280 +148,312 @@ public class IdCanvas extends JPanel * DOCUMENT ME! * * @param vertical - * DOCUMENT ME! + * DOCUMENT ME! */ public void fastPaint(int vertical) { - if (gg == null) + /* + * for now, not attempting fast paint of wrapped ids... + */ + if (gg == null || av.getWrapAlignment()) { repaint(); return; } - gg.copyArea(0, 0, getWidth(), imgHeight, 0, -vertical * av.charHeight); + ViewportRanges ranges = av.getRanges(); - int ss = av.startSeq; - int es = av.endSeq; + gg.copyArea(0, 0, getWidth(), imgHeight, 0, + -vertical * av.getCharHeight()); + + int ss = ranges.getStartSeq(); + int es = ranges.getEndSeq(); int transY = 0; if (vertical > 0) // scroll down { ss = es - vertical; - if (ss < av.startSeq) + if (ss < ranges.getStartSeq()) { // ie scrolling too fast, more than a page at a time - ss = av.startSeq; + ss = ranges.getStartSeq(); } else { - transY = imgHeight - (vertical * av.charHeight); + transY = imgHeight - ((vertical + 1) * av.getCharHeight()); } } - else if (vertical < 0) + else if (vertical < 0) // scroll up { es = ss - vertical; - if (es > av.endSeq) + if (es > ranges.getEndSeq()) { - es = av.endSeq; + es = ranges.getEndSeq(); } } gg.translate(0, transY); - drawIds(ss, es); + drawIds(gg, av, ss, es, searchResults); gg.translate(0, -transY); fastPaint = true; - repaint(); + + // Call repaint on alignment panel so that repaints from other alignment + // panel components can be aggregated. Otherwise performance of the overview + // window and others may be adversely affected. + av.getAlignPanel().repaint(); } /** * DOCUMENT ME! * * @param g - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void paintComponent(Graphics g) { + super.paintComponent(g); + g.setColor(Color.white); g.fillRect(0, 0, getWidth(), getHeight()); - + if (fastPaint) { fastPaint = false; g.drawImage(image, 0, 0, this); - + return; } - + int oldHeight = imgHeight; - + imgHeight = getHeight(); - imgHeight -= (imgHeight % av.charHeight); - + imgHeight -= (imgHeight % av.getCharHeight()); + if (imgHeight < 1) { return; } - + if (oldHeight != imgHeight || image.getWidth(this) != getWidth()) { - image = new BufferedImage(getWidth(), imgHeight, - BufferedImage.TYPE_INT_RGB); + image = new BufferedImage(getWidth(), imgHeight, + BufferedImage.TYPE_INT_RGB); } - + gg = (Graphics2D) image.getGraphics(); - + // Fill in the background gg.setColor(Color.white); gg.fillRect(0, 0, getWidth(), imgHeight); - - drawIds(av.getStartSeq(), av.endSeq); - + + drawIds(gg, av, av.getRanges().getStartSeq(), av.getRanges().getEndSeq(), searchResults); + g.drawImage(image, 0, 0, this); } /** - * DOCUMENT ME! + * Draws sequence ids from sequence index startSeq to endSeq (inclusive), with + * the font and other display settings configured on the viewport. Ids of + * sequences included in the selection are coloured grey, otherwise the + * current id colour for the sequence id is used. * - * @param starty - * DOCUMENT ME! - * @param endy - * DOCUMENT ME! + * @param g + * @param alignViewport + * @param startSeq + * @param endSeq + * @param selection */ - void drawIds(int starty, int endy) + void drawIds(Graphics2D g, AlignViewport alignViewport, final int startSeq, + final int endSeq, List selection) { - if (av.seqNameItalics) + Font font = alignViewport.getFont(); + if (alignViewport.isSeqNameItalics()) { - idfont = new Font(av.getFont().getName(), Font.ITALIC, av.getFont() - .getSize()); + setIdfont(new Font(font.getName(), Font.ITALIC, + font.getSize())); } else { - idfont = av.getFont(); + setIdfont(font); } - gg.setFont(idfont); - fm = gg.getFontMetrics(); + g.setFont(getIdfont()); + FontMetrics fm = g.getFontMetrics(); - if (av.antiAlias) + if (alignViewport.antiAlias) { - gg.setRenderingHint(RenderingHints.KEY_ANTIALIASING, + g.setRenderingHint(RenderingHints.KEY_ANTIALIASING, RenderingHints.VALUE_ANTIALIAS_ON); } Color currentColor = Color.white; Color currentTextColor = Color.black; - if (av.getWrapAlignment()) + boolean hasHiddenRows = alignViewport.hasHiddenRows(); + + if (alignViewport.getWrapAlignment()) { - int maxwidth = av.alignment.getWidth(); - int alheight = av.alignment.getHeight(); + drawIdsWrapped(g, alignViewport, startSeq, getHeight()); + return; + } - if (av.hasHiddenColumns) - { - maxwidth = av.getColumnSelection().findColumnPosition(maxwidth) - 1; - } + // Now draw the id strings + int panelWidth = getWidth(); + int xPos = 0; - int annotationHeight = 0; + // Now draw the id strings + for (int i = startSeq; i <= endSeq; i++) + { + SequenceI sequence = alignViewport.getAlignment().getSequenceAt(i); - if (av.showAnnotation) + if (sequence == null) { - if (ap == null) - { - ap = new AnnotationPanel(av); - } + continue; + } - annotationHeight = ap.adjustPanelHeight(); - if (labels == null) - { - labels = new AnnotationLabels(av); - } + if (hasHiddenRows || alignViewport.isDisplayReferenceSeq()) + { + g.setFont(getHiddenFont(sequence, alignViewport)); } - int hgap = av.charHeight; - if (av.scaleAboveWrapped) + // Selected sequence colours + if (selection != null && selection.contains(sequence)) + { + currentColor = Color.black; + currentTextColor = Color.white; + } + else if ((alignViewport.getSelectionGroup() != null) && alignViewport + .getSelectionGroup().getSequences(null).contains(sequence)) { - hgap += av.charHeight; + currentColor = Color.lightGray; + currentTextColor = Color.black; + } + else + { + currentColor = alignViewport.getSequenceColour(sequence); + currentTextColor = Color.black; } - int cHeight = alheight * av.charHeight + hgap + annotationHeight; + g.setColor(currentColor); - int rowSize = av.getEndRes() - av.getStartRes(); + int charHeight = alignViewport.getCharHeight(); + g.fillRect(0, (i - startSeq) * charHeight, + getWidth(), charHeight); - // Draw the rest of the panels - for (int ypos = hgap, row = av.startRes; (ypos <= getHeight()) - && (row < maxwidth); ypos += cHeight, row += rowSize) - { - for (int i = starty; i < alheight; i++) - { - SequenceI s = av.alignment.getSequenceAt(i); - if (av.hasHiddenRows) - { - setHiddenFont(s); - } - else - { - gg.setFont(idfont); - } - - drawIdString(gg, s, i, 0, ypos); - } + g.setColor(currentTextColor); - if (labels != null && av.showAnnotation) - { - gg.translate(0, ypos + (alheight * av.charHeight)); - labels.drawComponent(gg, getWidth()); - gg.translate(0, -ypos - (alheight * av.charHeight)); - } + String string = sequence + .getDisplayId(alignViewport.getShowJVSuffix()); + + if (alignViewport.isRightAlignIds()) + { + xPos = panelWidth - fm.stringWidth(string) - 4; } - } - else - { - // No need to hang on to labels if we're not wrapped - labels = null; - // Now draw the id strings - int panelWidth = getWidth(); - int xPos = 0; + g.drawString(string, xPos, (((i - startSeq) * charHeight) + charHeight) + - (charHeight / 5)); - SequenceI sequence; - // Now draw the id strings - for (int i = starty; i < endy; i++) + if (hasHiddenRows) { - sequence = av.alignment.getSequenceAt(i); - - if (sequence == null) - { - continue; - } + drawMarker(g, alignViewport, i, startSeq, 0); + } + } + } - if (av.hasHiddenRows) - { - setHiddenFont(sequence); - } + /** + * Draws sequence ids, and annotation labels if annotations are shown, in + * wrapped mode + * + * @param g + * @param alignViewport + * @param startSeq + */ + void drawIdsWrapped(Graphics2D g, AlignViewport alignViewport, + int startSeq, int pageHeight) + { + int alignmentWidth = alignViewport.getAlignment().getWidth(); + final int alheight = alignViewport.getAlignment().getHeight(); - // Selected sequence colours - if ((searchResults != null) && searchResults.contains(sequence)) - { - currentColor = Color.black; - currentTextColor = Color.white; - } - else if ((av.getSelectionGroup() != null) - && av.getSelectionGroup().getSequences(null).contains( - sequence)) - { - currentColor = Color.lightGray; - currentTextColor = Color.black; - } - else - { - currentColor = av.getSequenceColour(sequence); - currentTextColor = Color.black; - } + /* + * assumption: SeqCanvas.calculateWrappedGeometry has been called + */ + SeqCanvas seqCanvas = alignViewport.getAlignPanel() + .getSeqPanel().seqCanvas; - gg.setColor(currentColor); + final int charHeight = alignViewport.getCharHeight(); - gg.fillRect(0, (i - starty) * av.charHeight, getWidth(), - av.charHeight); + AnnotationLabels labels = null; + if (alignViewport.isShowAnnotation()) + { + labels = new AnnotationLabels(alignViewport); + } - gg.setColor(currentTextColor); + ViewportRanges ranges = alignViewport.getRanges(); - String string = sequence.getDisplayId(av.getShowJVSuffix()); + int rowSize = ranges.getViewportWidth(); - if (av.rightAlignIds) + /* + * draw repeating sequence ids until out of sequence data or + * out of visible space, whichever comes first + */ + boolean hasHiddenRows = alignViewport.hasHiddenRows(); + int ypos = seqCanvas.wrappedSpaceAboveAlignment; + int rowStartRes = ranges.getStartRes(); + while ((ypos <= pageHeight) && (rowStartRes < alignmentWidth)) + { + for (int i = startSeq; i < alheight; i++) + { + SequenceI s = alignViewport.getAlignment().getSequenceAt(i); + if (hasHiddenRows || alignViewport.isDisplayReferenceSeq()) { - xPos = panelWidth - fm.stringWidth(string) - 4; + g.setFont(getHiddenFont(s, alignViewport)); } - - gg.drawString(string, xPos, - (((i - starty) * av.charHeight) + av.charHeight) - - (av.charHeight / 5)); - - if (av.hasHiddenRows && av.showHiddenMarkers) + else { - drawMarker(i, starty, 0); + g.setFont(getIdfont()); } + drawIdString(g, hasHiddenRows, s, i, 0, ypos); + } + if (labels != null && alignViewport.isShowAnnotation()) + { + g.translate(0, ypos + (alheight * charHeight)); + labels.drawComponent(g, getWidth()); + g.translate(0, -ypos - (alheight * charHeight)); } + ypos += seqCanvas.wrappedRepeatHeightPx; + rowStartRes += rowSize; } } - void drawMarker(int i, int starty, int yoffset) + /** + * Draws a marker (a blue right-pointing triangle) between sequences to + * indicate hidden sequences. + * + * @param g + * @param alignViewport + * @param seqIndex + * @param starty + * @param yoffset + */ + void drawMarker(Graphics2D g, AlignViewport alignViewport, int seqIndex, int starty, int yoffset) { - - SequenceI[] hseqs = av.alignment.getHiddenSequences().hiddenSequences; + SequenceI[] hseqs = alignViewport.getAlignment() + .getHiddenSequences().hiddenSequences; // Use this method here instead of calling hiddenSeq adjust // 3 times. int hSize = hseqs.length; - int hiddenIndex = i; - int lastIndex = i - 1; - int nextIndex = i + 1; + int hiddenIndex = seqIndex; + int lastIndex = seqIndex - 1; + int nextIndex = seqIndex + 1; for (int j = 0; j < hSize; j++) { @@ -429,61 +474,110 @@ public class IdCanvas extends JPanel } } + /* + * are we below or above the hidden sequences? + */ boolean below = (hiddenIndex > lastIndex + 1); boolean above = (nextIndex > hiddenIndex + 1); - gg.setColor(Color.blue); + g.setColor(Color.blue); + int charHeight = av.getCharHeight(); + + /* + * vertices of the triangle, below or above hidden seqs + */ + int[] xPoints = new int[] + { getWidth() - charHeight, + getWidth() - charHeight, getWidth() }; + int yShift = seqIndex - starty; + if (below) { - gg.fillPolygon( - new int[] - { getWidth() - av.charHeight, getWidth() - av.charHeight, - getWidth() }, new int[] - { - (i - starty) * av.charHeight + yoffset, - (i - starty) * av.charHeight + yoffset + av.charHeight - / 4, (i - starty) * av.charHeight + yoffset }, 3); + int[] yPoints = new int[] { yShift * charHeight + yoffset, + yShift * charHeight + yoffset + charHeight / 4, + yShift * charHeight + yoffset }; + g.fillPolygon(xPoints, yPoints, 3); } if (above) { - gg.fillPolygon( - new int[] - { getWidth() - av.charHeight, getWidth() - av.charHeight, - getWidth() }, new int[] - { - (i - starty + 1) * av.charHeight + yoffset, - (i - starty + 1) * av.charHeight + yoffset - - av.charHeight / 4, - (i - starty + 1) * av.charHeight + yoffset }, 3); - + yShift++; + int[] yPoints = new int[] { yShift * charHeight + yoffset, + yShift * charHeight + yoffset - charHeight / 4, + yShift * charHeight + yoffset }; + g.fillPolygon(xPoints, yPoints, 3); } } - void setHiddenFont(SequenceI seq) + /** + * Answers the standard sequence id font, or a bold font if the sequence is + * set as reference or a hidden group representative + * + * @param seq + * @param alignViewport + * @return + */ + private Font getHiddenFont(SequenceI seq, AlignViewport alignViewport) { - Font bold = new Font(av.getFont().getName(), Font.BOLD, av.getFont() - .getSize()); - - if (av.hiddenRepSequences != null - && av.hiddenRepSequences.containsKey(seq)) + if (av.isReferenceSeq(seq) || av.isHiddenRepSequence(seq)) { - gg.setFont(bold); - } - else - { - gg.setFont(idfont); + return new Font(av.getFont().getName(), Font.BOLD, + av.getFont().getSize()); } + return getIdfont(); } /** * DOCUMENT ME! * - * @param found - * DOCUMENT ME! + * @param list + * DOCUMENT ME! */ - public void setHighlighted(java.util.Vector found) + public void setHighlighted(List list) { - searchResults = found; + searchResults = list; repaint(); } + + public Font getIdfont() + { + return idfont; + } + + public void setIdfont(Font idfont) + { + this.idfont = idfont; + } + + /** + * Respond to viewport range changes (e.g. alignment panel was scrolled). Both + * scrolling and resizing change viewport ranges. Scrolling changes both start + * and end points, but resize only changes end values. Here we only want to + * fastpaint on a scroll, with resize using a normal paint, so scroll events + * are identified as changes to the horizontal or vertical start value. + *

+ * In unwrapped mode, only responds to a vertical scroll, as horizontal scroll + * leaves sequence ids unchanged. In wrapped mode, only vertical scroll is + * provided, but it generates a change of "startres" which does require an + * update here. + */ + @Override + public void propertyChange(PropertyChangeEvent evt) + { + String propertyName = evt.getPropertyName(); + if (propertyName.equals(ViewportRanges.STARTSEQ) + || (av.getWrapAlignment() + && propertyName.equals(ViewportRanges.STARTRES))) + { + fastPaint((int) evt.getNewValue() - (int) evt.getOldValue()); + } + else if (propertyName.equals(ViewportRanges.STARTRESANDSEQ)) + { + fastPaint(((int[]) evt.getNewValue())[1] + - ((int[]) evt.getOldValue())[1]); + } + else if (propertyName.equals(ViewportRanges.MOVE_VIEWPORT)) + { + repaint(); + } + } }